From: Rossen Apostolov Date: Thu, 20 Feb 2014 16:21:50 +0000 (+0100) Subject: Removed deprecated Encad FF. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=84af95977f94f8e7f29b2e8bd57308fcffba6718;p=alexxy%2Fgromacs.git Removed deprecated Encad FF. Change-Id: Ib7f5c3d9920307a808dde9ef13b0f042827eb8ca --- diff --git a/share/top/encads.ff/aminoacids.c.tdb b/share/top/encads.ff/aminoacids.c.tdb deleted file mode 100644 index b06deead13..0000000000 --- a/share/top/encads.ff/aminoacids.c.tdb +++ /dev/null @@ -1,44 +0,0 @@ -[ None ] - -[ COO- ] -[ replace ] -C C Abis 12.011 0.84 -O O1 Obis 15.9994 -0.92 -OXT O2 Obis 15.9994 -0.92 -[ add ] -2 8 O C CA N - Obis 15.9994 -0.92 -[ dihedrals ] -N CA C O2 -[ impropers ] -CA O2 C O1 improper_X_X_A_X -N C CA CB improper_X_X_C_X - -[ Gly-COO- ] -[ replace ] -C C Abis 12.011 0.84 -O O Obis 15.9994 -0.92 -OXT O2 Obis 15.9994 -0.92 -[ add ] -2 8 O C CA N - Obis 15.9994 -0.92 -[ dihedrals ] -N CA C O2 -[ impropers ] -CA O2 C O1 improper_X_X_A_X - -[ COOH ] -[ replace ] -C C Aprime 12.011 0.38 -O O OH 15.9994 -0.38 -OXT OT O 15.9994 -0.433 -[ add ] -1 2 OT C CA N - O 15.9994 -0.433 -1 2 HO O C CA - HO 1.008 0.433 -[ dihedrals ] -N CA C O -[ impropers ] -OT CA C O improper_X_X_A_X - diff --git a/share/top/encads.ff/aminoacids.hdb b/share/top/encads.ff/aminoacids.hdb deleted file mode 100644 index 06e00b703f..0000000000 --- a/share/top/encads.ff/aminoacids.hdb +++ /dev/null @@ -1,189 +0,0 @@ -ACE 1 -3 4 HH3 CH3 C O -ALA 3 -1 1 H N -C CA -1 5 HA CA N C CB -3 4 HB CB CA N -ARG 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD NE CG -1 1 HE NE CD CZ -2 3 HH1 NH1 CZ NE -2 3 HH2 NH2 CZ NE -ARGN 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD NE CG -1 1 HE NE CD CZ -1 2 HH1 NH1 CZ NE -2 3 HH2 NH2 CZ NE -ASN 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 3 HD2 ND2 CG CB -ASP 3 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -ASPH 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 2 HD2 OD2 CG CB -CYS2 3 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB SG CA -CYSH 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB SG CA -1 2 HG SG CB CA -GLN 5 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 3 HE2 NE2 CD CG -GLU 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -GLUH 5 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -1 2 HE2 OE2 CD CG -GLY 2 -1 1 H N -C CA -2 6 HA CA C N -HIS1 6 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -1 1 HD1 ND1 CG CE1 -HISA 6 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -1 1 HD1 ND1 CG CE1 -HISB 6 -1 1 H N -C CA -2 6 HB CB CG CA -1 5 HA CA N C CB -1 1 HE2 NE2 CE1 CD2 -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -HISH 7 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -1 1 HD1 ND1 CG CE1 -1 1 HE2 NE2 CE1 CD2 -HOH 1 -2 7 HW OW -ILE 6 -1 1 H N -C CA -1 5 HA CA N C CB -1 5 HB CB CA CG1 CG2 -2 6 HG1 CG1 CD CB -3 4 HG2 CG2 CB CA -3 4 HD CD CG1 CB -LEU 6 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 5 HG CG CB CD1 CD2 -3 4 HD1 CD1 CG CB -3 4 HD2 CD2 CG CB -LYS 7 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD CE CG -2 6 HE CE NZ CD -2 4 HZ NZ CE CD -LYSH 7 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD CE CG -2 6 HE CE NZ CD -3 4 HZ NZ CE CD -MET 5 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG SD CB -3 4 HE CE SD CG -NAC 2 -1 1 H N -C CA -3 4 HA CA N -C -NH2 1 -2 3 H N -C -CA -PHE 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD1 CD1 CG CE1 -1 1 HD2 CD2 CG CE2 -1 1 HE1 CE1 CD1 CZ -1 1 HE2 CE2 CD2 CZ -1 1 HZ CZ CE1 CE2 -PRO 4 -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD N CG -SER 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB OG CA -1 2 HG OG CB CA -THR 5 -1 1 H N -C CA -1 5 HA CA N C CB -1 5 HB CB CA OG1 CG2 -1 2 HG1 OG1 CB CA -3 4 HG2 CG2 CB CA -TRP 9 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD1 CD1 NE1 CG -1 1 HE1 NE1 CD1 CE2 -1 1 HE3 CE3 CD2 CZ3 -1 1 HZ3 CZ3 CE3 CH2 -1 1 HH2 CH2 CZ3 CZ2 -1 1 HZ2 CZ2 CE2 CH2 -TYR 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD1 CD1 CG CE1 -1 1 HD2 CD2 CG CE2 -1 1 HE1 CE1 CD1 CZ -1 1 HE2 CE2 CD2 CZ -1 2 HH OH CZ CE1 -VAL 5 -1 1 H N -C CA -1 5 HA CA N C CB -1 5 HB CB CA CG1 CG2 -3 4 HG1 CG1 CB CA -3 4 HG2 CG2 CB CA diff --git a/share/top/encads.ff/aminoacids.n.tdb b/share/top/encads.ff/aminoacids.n.tdb deleted file mode 100644 index a532d316ff..0000000000 --- a/share/top/encads.ff/aminoacids.n.tdb +++ /dev/null @@ -1,49 +0,0 @@ -[ None ] - -[ NH3+ ] -[ replace ] -N M3 14.0067 -0.71 -[ add ] -3 4 H N CA C - HN 1.008 0.57 -[ delete ] -H -[ dihedrals ] -H1 N CA C -[ impropers ] -H1 CA N H2 improper_X_X_M3_X -H1 CA N H3 improper_X_X_M3_X - -[ NH2 ] -[ replace ] -N N2 14.0067 -0.666 -[ add ] -2 4 H N CA C - HN 1.008 0.333 -[ delete ] -H -[ dihedrals ] -H1 N CA C -[ impropers ] -H1 CA N H2 improper_X_X_M_X - -[ PRO-NH2+ ] -[ replace ] -N N2 14.0067 -0.14 -[ add ] -2 4 H N CA C - HN 1.008 0.57 -[ dihedrals ] -H1 N CA C -[ impropers ] -H1 CA N H2 improper_X_X_M_X - -[ PRO-NH ] -[ replace ] -N N1 14.0067 -0.333 -[ add ] -1 4 H N CA C - HN 1.008 0.333 -[ dihedrals ] -H1 N CA C - diff --git a/share/top/encads.ff/aminoacids.r2b b/share/top/encads.ff/aminoacids.r2b deleted file mode 100644 index 823db9041c..0000000000 --- a/share/top/encads.ff/aminoacids.r2b +++ /dev/null @@ -1,7 +0,0 @@ -; rtp residue to rtp building block table -;GMX Force-field -CYS CYSH -HISD HISA -HISE HISB -LYS LYSH -LYSN LYS diff --git a/share/top/encads.ff/aminoacids.rtp b/share/top/encads.ff/aminoacids.rtp deleted file mode 100644 index a23099b5d4..0000000000 --- a/share/top/encads.ff/aminoacids.rtp +++ /dev/null @@ -1,1919 +0,0 @@ -; -; Encad residue topology file. -; Note that this is only a subset of all molecules described -; in Encad. If you need to use a new one, it might help to -; study the parameter files of Encad. -; -[ bondedtypes ] -; Column 1 : default bondtype -; Column 2 : default angletype -; Column 3 : default proper dihedraltype -; Column 4 : default improper dihedraltype -; Column 5 : This controls the generation of dihedrals from the bonding. -; All possible dihedrals are generated automatically. A value of -; 1 here means that all these are retained. A value of -; 0 here requires generated dihedrals be removed if -; * there are any dihedrals on the same central atoms -; specified in the residue topology, or -; * there are other identical generated dihedrals -; sharing the same central atoms, or -; * there are other generated dihedrals sharing the -; same central bond that have fewer hydrogen atoms -; Column 6 : number of neighbors to exclude from non-bonded interactions -; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms -; 0 = do not generate such -; Column 8 : 1 = remove proper dihedrals if found centered on the same -; bond as an improper dihedral -; 0 = do not generate such -; bonds angles dihedrals impropers all_dihedrals nrexcl bHH14 bRemoveDih - 1 1 1 1 0 3 1 - - -[ ACE ] - [ atoms ] - CH3 C3 -0.357 1 - HH31 H 0.119 1 - HH32 H 0.119 1 - HH33 H 0.119 1 - C Aprime 0.380 2 - O O -0.380 2 - [ bonds ] - CH3 HH31 - CH3 HH32 - CH3 HH33 - CH3 C - C O -[ dihedrals ] - HH33 CH3 C +N - CH3 C +N +CA -[ impropers ] - C HH33 CH3 HH31 improper_X_X_C_X - C HH33 CH3 HH32 improper_X_X_C_X - CH3 +N C O improper_X_X_A_X - - -[ ALA ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C3 -0.357 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - HB3 H 0.119 2 - C Aprime 0.380 3 - O O -0.380 3 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB HB3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB HB3 - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA HB3 CB HB1 improper_X_X_C_X - CA HB3 CB HB2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ ARG ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - NE M1 -0.333 5 - HE HN 0.533 5 - CZ A6 0.000 6 - NH1 M2 -0.666 7 - HH11 HN 0.533 7 - HH12 HN 0.533 7 - NH2 M2 -0.666 8 - HH21 HN 0.533 8 - HH22 HN 0.533 8 - C Aprime 0.380 9 - O O -0.380 9 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD NE - NE HE - NE CZ - CZ NH1 - CZ NH2 - NH1 HH11 - NH1 HH12 - NH2 HH21 - NH2 HH22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD NE - CG CD NE CZ - CD NE CZ NH2 - NE CZ NH1 HH12 - NE CZ NH2 HH22 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG NE CD HD1 improper_X_X_C_X - CG NE CD HD2 improper_X_X_C_X - CD CZ NE HE improper_X_X_M_X - NE NH2 CZ NH1 improper_X_X_A_X - CZ HH12 NH1 HH11 improper_X_X_M_X - CZ HH22 NH2 HH21 improper_X_X_M_X - - -[ ARGN ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - NE M1 -0.333 5 - HE HN 0.333 5 - CZ A6 0.000 6 - NH1 M1 -0.333 7 - HH1 HN 0.333 7 - NH2 M2 -0.666 8 - HH21 HN 0.333 8 - HH22 HN 0.333 8 - C Aprime 0.380 9 - O O -0.380 9 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD NE - NE HE - NE CZ - CZ NH1 - CZ NH2 - NH1 HH1 - NH2 HH21 - NH2 HH22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD NE - CG CD NE CZ - CD NE CZ NH2 - NE CZ NH1 HH1 - NE CZ NH2 HH22 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG NE CD HD1 improper_X_X_C_X - CG NE CD HD2 improper_X_X_C_X - CD CZ NE HE improper_X_X_M_X - NE NH1 CZ NH2 improper_X_X_A_X - CZ HH21 NH2 HH22 improper_X_X_M_X - - -[ ASN ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG Aprime 0.380 3 - OD1 O -0.380 3 - ND2 N2 -0.666 4 - HD21 HN 0.333 4 - HD22 HN 0.333 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG OD1 - CG ND2 - ND2 HD21 - ND2 HD22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG ND2 - CB CG ND2 HD22 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB ND2 CG OD1 improper_X_X_A_X - CG HD22 ND2 HD21 improper_X_X_N_X - - -[ ASP ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG Abis 0.840 3 - OD1 Obis -0.920 3 - OD2 Obis -0.920 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG OD1 - CG OD2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG OD2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB OD2 CG OD1 improper_X_X_A_X - - -[ ASPH ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG Aprime 0.380 3 - OD1 O -0.380 3 - OD2 OH -0.433 4 - HD2 HO 0.433 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG OD1 - CG OD2 - OD2 HD2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG OD2 - CB CG OD2 HD2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - OD2 CB CG OD1 improper_X_X_A_X - - - -[ CYS2 ] ; aka CYX - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - SG S 0.000 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB SG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB SG - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA SG CB HB1 improper_X_X_C_X - CA SG CB HB2 improper_X_X_C_X - - -[ CYSH ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - SG SH -0.200 3 - HG H 0.200 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB SG - SG HG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB SG - CA CB SG HG - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA SG CB HB1 improper_X_X_C_X - CA SG CB HB2 improper_X_X_C_X - - -[ CYH ] ; same as cysh - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - SG SH -0.200 3 - HG H 0.200 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB SG - SG HG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB SG - CA CB SG HG - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA SG CB HB1 improper_X_X_C_X - CA SG CB HB2 improper_X_X_C_X - - - -[ GLN ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD Aprime 0.380 4 - OE1 O -0.380 4 - NE2 N2 -0.666 5 - HE21 HN 0.333 5 - HE22 HN 0.333 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD OE1 - CD NE2 - NE2 HE21 - NE2 HE22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - CA CB CG CD - CB CG CD NE2 - CG CD NE2 HE22 - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG NE2 CD OE1 improper_X_X_A_X - CD HE22 NE2 HE21 improper_X_X_N_X - - -[ GLU ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD Abis 0.840 4 - OE1 Obis -0.920 4 - OE2 Obis -0.920 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD OE1 - CD OE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD OE2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG OE2 CD OE1 improper_X_X_A_X - - -[ GLUH ] - [ atoms ] - N N1 -0.333 1 - H HN 0.333 1 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD Aprime 0.380 4 - OE1 O -0.380 4 - OE2 OH -0.433 5 - HE2 HO 0.433 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD OE1 - CD OE2 - OE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD OE2 - CG CD OE2 HE2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG OE2 CD OE1 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ GLY ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C2 -0.238 1 - HA1 H 0.119 1 - HA2 H 0.119 1 - C Aprime 0.380 2 - O O -0.380 2 - [ bonds ] - N H - N CA - CA HA1 - CA HA2 - CA C - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA1 improper_X_X_C_X - N C CA HA2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ HISA ] ; A.K.A. HISD/HID - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.333 4 - HD1 HN 0.333 4 - CE1 A5 0.081 5 - HE1 H 0.119 5 - NE2 L5 -0.400 5 - CD2 A5 0.081 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HID ] ; same as HISA - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.333 4 - HD1 HN 0.333 4 - CE1 A5 0.081 5 - HE1 H 0.119 5 - NE2 L5 -0.400 5 - CD2 A5 0.081 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HIS1 ] Identical to HISA - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.333 4 - HD1 HN 0.333 4 - CE1 A5 0.081 5 - HE1 H 0.119 5 - NE2 L5 -0.400 5 - CD2 A5 0.081 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ HISB ] ; A.K.A. HISE/HIE - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.200 3 - ND1 L5 -0.400 3 - CE1 A5 0.081 3 - HE1 H 0.119 3 - NE2 N1 -0.333 4 - HE2 HN 0.333 4 - CD2 A5 -0.119 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - NE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - CE1 CD2 NE2 HE2 improper_X_X_N_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ HIE ] ; same as HISB - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.200 3 - ND1 L5 -0.400 3 - CE1 A5 0.081 3 - HE1 H 0.119 3 - NE2 N1 -0.333 4 - HE2 HN 0.333 4 - CD2 A5 -0.119 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - NE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - CE1 CD2 NE2 HE2 improper_X_X_N_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HISH ] ; also known as HISP (or HIS+) - [ atoms ] - N N1 -0.333 1 - H HN 0.333 1 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.200 3 - ND1 N1 -0.300 3 - HD1 HN 0.375 3 - CE1 A5 0.206 3 - HE1 H 0.119 3 - NE2 N1 -0.300 3 - HE2 HN 0.375 3 - CD2 A5 0.206 3 - HD2 H 0.119 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - NE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - CE1 CD2 NE2 HE2 improper_X_X_N_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HOH ] -; SPC and encad water have identical charges. -; Include encadwater.itp instead of spc.itp to use the flexible encad bonds/angles -; instead of the rigid SPC model. - [ atoms ] - OW OW -0.82 0 - HW1 HW 0.41 0 - HW2 HW 0.41 0 - [ bonds ] - OW HW1 - OW HW2 - - -[ ILE ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C1 -0.119 2 - HB H 0.119 2 - CG2 C3 -0.357 3 - HG21 H 0.119 3 - HG22 H 0.119 3 - HG23 H 0.119 3 - CG1 C2 -0.238 4 - HG11 H 0.119 4 - HG12 H 0.119 4 - CD C3 -0.357 5 - HD1 H 0.119 5 - HD2 H 0.119 5 - HD3 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB - CB CG1 - CB CG2 - CG1 HG11 - CG1 HG12 - CG1 CD - CG2 HG21 - CG2 HG22 - CG2 HG23 - CD HD1 - CD HD2 - CD HD3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG1 - N CA C +N - CA CB CG2 HG23 - CA CB CG1 CD - CB CG1 CD HD3 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG1 CB CG2 improper_C1_C2_C1_C3 - CA CG1 CB HB improper_X_X_C_X - CB CD CG1 HG11 improper_X_X_C_X - CB CD CG1 HG12 improper_X_X_C_X - CG1 HD3 CD HD1 improper_X_X_C_X - CG1 HD3 CD HD2 improper_X_X_C_X - CB HG23 CG2 HG21 improper_X_X_C_X - CB HG23 CG2 HG22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ LEU ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C1 -0.119 3 - HG H 0.119 3 - CD1 C3 -0.357 4 - HD11 H 0.119 4 - HD12 H 0.119 4 - HD13 H 0.119 4 - CD2 C3 -0.357 5 - HD21 H 0.119 5 - HD22 H 0.119 5 - HD23 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG - CG CD1 - CG CD2 - CD1 HD11 - CD1 HD12 - CD1 HD13 - CD2 HD21 - CD2 HD22 - CD2 HD23 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 HD13 - CB CG CD2 HD23 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG HG improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_C_X - CG HD13 CD1 HD11 improper_X_X_C_X - CG HD13 CD1 HD12 improper_X_X_C_X - CG HD23 CD2 HD21 improper_X_X_C_X - CG HD23 CD2 HD22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ LYS ] ; non-protonated - see LYSH for the most common state. - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - CE C2 -0.238 5 - HE1 H 0.119 5 - HE2 H 0.119 5 - NZ N2 -0.666 6 - HZ1 HN 0.333 6 - HZ2 HN 0.333 6 - C Aprime 0.380 7 - O O -0.380 7 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD CE - CE HE1 - CE HE2 - CE NZ - NZ HZ1 - NZ HZ2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD CE - CG CD CE NZ - CD CE NZ HZ2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG CE CD HD1 improper_X_X_C_X - CG CE CD HD2 improper_X_X_C_X - CD NZ CE HE1 improper_X_X_C_X - CD NZ CE HE2 improper_X_X_C_X - CE HZ2 NZ HZ1 improper_X_X_M_X - CA +N C O improper_X_X_A_X - - - -[ LYSH ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - CE C2 -0.238 5 - HE1 H 0.119 5 - HE2 H 0.119 5 - NZ M3 -0.710 6 - HZ1 HN 0.570 6 - HZ2 HN 0.570 6 - HZ3 HN 0.570 6 - C Aprime 0.380 7 - O O -0.380 7 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD CE - CE HE1 - CE HE2 - CE NZ - NZ HZ1 - NZ HZ2 - NZ HZ3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD CE - CG CD CE NZ - CD CE NZ HZ3 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG CE CD HD1 improper_X_X_C_X - CG CE CD HD2 improper_X_X_C_X - CD NZ CE HE1 improper_X_X_C_X - CD NZ CE HE2 improper_X_X_C_X - CE HZ3 NZ HZ1 improper_X_X_M3_X - CE HZ3 NZ HZ2 improper_X_X_M3_X - CA +N C O improper_X_X_A_X - - -[ MET ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - SD S 0.000 4 - CE C3 -0.357 5 - HE1 H 0.119 5 - HE2 H 0.119 5 - HE3 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG SD - SD CE - CE HE1 - CE HE2 - CE HE3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG SD - CB CG SD CE - CG SD CE HE3 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB SD CG HG1 improper_X_X_C_X - CB SD CG HG2 improper_X_X_C_X - SD HE3 CE HE1 improper_X_X_C_X - SD HE3 CE HE2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ NAC ] ; metylamide, a.k.a NMA. - [ atoms ] - N N1 -0.333 1 - H HN 0.333 1 - CH3 C3 -0.357 2 - HH31 H 0.119 2 - HH32 H 0.119 2 - HH33 H 0.119 2 - [ bonds ] - N H - N CH3 - CH3 HH31 - CH3 HH32 - CH3 HH33 - -C N - [ dihedrals ] - -CA -C N CH3 - -C N CH3 HH33 - [ impropers ] - -C CH3 N H improper_X_X_N_X - N HH33 CH3 HH31 improper_X_X_C_X - N HH33 CH3 HH32 improper_X_X_C_X - - -[ NH2 ] - [ atoms ] - N N2 -0.666 1 - H1 HN 0.333 1 - H2 HN 0.333 1 - [ bonds ] - -C N - N H1 - N H2 - [ dihedrals ] - -CA -C N H2 - [ impropers ] - -C H2 N H1 improper_X_X_N_X - - -[ NHE ] -; same as NH2 - [ atoms ] - N N2 -0.666 1 - H1 HN 0.333 1 - H2 HN 0.333 1 - [ bonds ] - -C N - N H1 - N H2 - [ dihedrals ] - -CA -C N H2 - [ impropers ] - -C H2 N H1 improper_X_X_N_X - - -[ PHE ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A6 0.000 3 - CD1 A6 -0.119 4 - HD1 H 0.119 4 - CE1 A6 -0.119 5 - HE1 H 0.119 5 - CZ A6 -0.119 6 - HZ H 0.119 6 - CE2 A6 -0.119 7 - HE2 H 0.119 7 - CD2 A6 -0.119 8 - HD2 H 0.119 8 - C Aprime 0.380 9 - O O -0.380 9 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG CD1 - CG CD2 - CD1 HD1 - CD1 CE1 - CD2 HD2 - CD2 CE2 - CE1 HE1 - CE1 CZ - CE2 HE2 - CE2 CZ - CZ HZ - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 CE1 - CB CG CD2 CE2 - CG CD1 CE1 CZ - CD1 CE1 CZ CE2 - CE1 CZ CE2 CD2 - CZ CE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_A_X - CG CE1 CD1 HD1 improper_X_X_A_X - CD1 CZ CE1 HE1 improper_X_X_A_X - CE1 CE2 CZ HZ improper_X_X_A_X - CE2 CG CD2 HD2 improper_X_X_A_X - CZ CD2 CE2 HE2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ PRO ] - [ atoms ] - N N 0.000 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB CP -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG CP -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD CP -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD N - C O - -C N - [ dihedrals ] - -CA -C N CD - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD N - [ impropers ] - -C CA N CD improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG N CD HD1 improper_X_X_C_X - CG N CD HD2 improper_X_X_C_X - -C CD N CA improper_X_X_N_X - CA +N C O improper_X_X_A_X - - - -[ SER ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - OG OH -0.433 3 - HG HO 0.433 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB OG - OG HG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB OG - N CA C +N - CA CB OG HG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA OG CB HB1 improper_X_X_C_X - CA OG CB HB2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ THR ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C1 -0.119 2 - HB H 0.119 2 - OG1 OH -0.433 3 - HG1 HO 0.433 3 - CG2 C3 -0.357 4 - HG21 H 0.119 4 - HG22 H 0.119 4 - HG23 H 0.119 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB - CB OG1 - CB CG2 - OG1 HG1 - CG2 HG21 - CG2 HG22 - CG2 HG23 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG2 - N CA C +N - CA CB OG1 HG1 - CA CB CG2 HG23 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG2 CB OG1 improper_X_X_C_X - CA CG2 CB HB improper_X_X_C_X - CB HG23 CG2 HG21 improper_X_X_C_X - CB HG23 CG2 HG22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ TRP ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - CD1 A5 -0.119 4 - HD1 H 0.119 4 - NE1 N1 -0.333 5 - HE1 HN 0.333 5 - CE2 A7 0.000 6 - CZ2 A6 -0.119 7 - HZ2 H 0.119 7 - CH2 A6 -0.119 8 - HH2 H 0.119 8 - CZ3 A6 -0.119 9 - HZ3 H 0.119 9 - CE3 A6 -0.119 10 - HE3 H 0.119 10 - CD2 A7 0.000 11 - C Aprime 0.380 12 - O O -0.380 12 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG CD1 - CG CD2 - CD1 HD1 - CD1 NE1 - CD2 CE2 - CD2 CE3 - NE1 HE1 - NE1 CE2 - CE2 CZ2 - CE3 HE3 - CE3 CZ3 - CZ2 HZ2 - CZ2 CH2 - CZ3 HZ3 - CZ3 CH2 - CH2 HH2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 NE1 - CG CD1 NE1 CE2 - CD1 NE1 CE2 CD2 - NE1 CE2 CD2 CE3 - NE1 CE2 CZ2 CH2 - CE2 CZ2 CH2 CZ3 - CZ2 CH2 CZ3 CE3 - CH2 CZ3 CE3 CD2 - CZ3 CE3 CD2 CE2 - CB CG CD2 CE3 - [ impropers ] - -C CA N H improper_X_X_N_X - CA +N C O improper_X_X_A_X - N C CA CB improper_N_A_C1_C - N C CA HA improper_X_X_C_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_A_X - CG NE1 CD1 HD1 improper_X_X_A_X - CD1 CE2 NE1 HE1 improper_X_X_N_X - NE1 CD2 CE2 CZ2 improper_X_X_A_X - CE2 CH2 CZ2 HZ2 improper_X_X_A_X - CZ2 CZ3 CH2 HH2 improper_X_X_A_X - CH2 CE3 CZ3 HZ3 improper_X_X_A_X - CZ3 CD2 CE3 HE3 improper_X_X_A_X - CG CD2 CE2 CE3 improper_X_X_A_X - - -[ TYR ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A6 0.000 3 - CD1 A6 -0.119 4 - HD1 H 0.119 4 - CE1 A6 -0.119 5 - HE1 H 0.119 5 - CZ A6 0.000 6 - OH OH -0.433 7 - HH HO 0.433 7 - CE2 A6 -0.119 8 - HE2 H 0.119 8 - CD2 A6 -0.119 9 - HD2 H 0.119 9 - C Aprime 0.380 10 - O O -0.380 10 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG CD1 - CG CD2 - CD1 HD1 - CD1 CE1 - CD2 HD2 - CD2 CE2 - CE1 HE1 - CE1 CZ - CE2 HE2 - CE2 CZ - CZ OH - OH HH - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 CE1 - CB CG CD2 CE2 - CG CD1 CE1 CZ - CD1 CE1 CZ CE2 - CE1 CZ OH HO - CE1 CZ CE2 CD2 - CZ CE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_A_X - CG CE1 CD1 HD1 improper_X_X_A_X - CD1 CZ CE1 HE1 improper_X_X_A_X - CE1 CE2 CZ OH improper_X_X_A_X - CE2 CG CD2 HD2 improper_X_X_A_X - CZ CD2 CE2 HE2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - - -[ VAL ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C1 -0.119 2 - HB H 0.119 2 - CG1 C3 -0.357 3 - HG11 H 0.119 3 - HG12 H 0.119 3 - HG13 H 0.119 3 - CG2 C3 -0.357 4 - HG21 H 0.119 4 - HG22 H 0.119 4 - HG23 H 0.119 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB - CB CG1 - CB CG2 - CG1 HG11 - CG1 HG12 - CG1 HG13 - CG2 HG21 - CG2 HG22 - CG2 HG23 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG2 - N CA C +N - CA CB CG2 HG23 - CA CB CG1 HG13 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG2 CB HB improper_X_X_C_X - CA CG2 CB CG1 improper_X_X_C_X - CB HG13 CG1 HG11 improper_X_X_C_X - CB HG13 CG1 HG12 improper_X_X_C_X - CB HG23 CG2 HG21 improper_X_X_C_X - CB HG23 CG2 HG22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ CL ] - [ atoms ] - CL CL -1.000 0 - -[ NA ] - [ atoms ] - NA NA 1.000 0 - -[ FE ] - [ atoms ] - FE FE 2.000 0 - -[ Ar ] - [ atoms ] - AR AR 0.000 0 - diff --git a/share/top/encads.ff/atomtypes.atp b/share/top/encads.ff/atomtypes.atp deleted file mode 100644 index 719113ed1f..0000000000 --- a/share/top/encads.ff/atomtypes.atp +++ /dev/null @@ -1,43 +0,0 @@ - H 1.008 ; Hydrogen bound to carbon - O 15.9994 ; Oxygen - N 14.0067 ; Trivalent nitrogen - N1 14.0067 ; Trivalent nitrogen - N2 14.0067 ; Trivalent nitrogen - C1 12.011 ; Aliphatic carbon - C2 12.011 ; Aliphatic carbon - C3 12.011 ; Aliphatic carbon - CP 12.011 ; Aliphatic carbon - A6 12.011 ; Aromatic carbon - A5 12.011 ; Aromatic carbon - A7 12.011 ; Aromatic carbon - Aprime 12.011 ; Aromatic carbon - Abis 12.011 ; Aromatic carbon - L5 14.0067 ; Acceptor nitrogen - L6 14.0067 ; Acceptor nitrogen - P 30.9738 ; Phosphorus - OH 15.9994 ; Divalent oxygen - O2 15.9994 ; Divalent oxygen - OR 15.9994 ; Divalent oxygen - S 32.060 ; Sulphur not bound to hydrogen - SH 32.060 ; Sulphur with bound hydrogen - M1 14.0067 ; Charged nitrogen - M2 14.0067 ; Charged nitrogen - M3 14.0067 ; Charged nitrogen - HN 1.008 ; Polar hydrogen - HO 1.008 ; Polar hydrogen - HW 1.008 ; Water hydrogen - CL 35.453 ; Chloride ion - Obis 15.9994 ; Charged oxygen - OP 15.9994 ; Charged oxygen - R 14.0067 ; Heme nitrogen - W 14.0067 ; Heme nitrogen - Y 12.011 ; Heme carbon - Z 12.011 ; Heme carbon - FE 55.847 ; Heme Iron - OF 15.9994 ; Heme oxygen - OW 15.9994 ; Water oxygen - AR 39.948 ; Argon - NA 22.9898 ; Sodium - MCH3 0 ; Dummy - MNH3 0 ; Dummy - MW 0 ; Dummy diff --git a/share/top/encads.ff/f3c.itp b/share/top/encads.ff/f3c.itp deleted file mode 100644 index d7def4ade0..0000000000 --- a/share/top/encads.ff/f3c.itp +++ /dev/null @@ -1,26 +0,0 @@ -; -; f3c water for use with the Encad force fields. -; - -[ moleculetype ] -; molname nrexcl -SOL 2 - -#ifdef _FF_ENCAD -[ atoms ] -; nr type resnr residue atom cgnr charge mass - 1 OW 1 SOL OW 1 -0.82 - 2 HW 1 SOL HW1 1 0.41 - 3 HW 1 SOL HW2 1 0.41 - -[ bonds ] -; i j funct length force.c. -1 2 1 0.1 209200 -1 3 1 0.1 209200 - -[ angles ] -; i j k funct angle force.c. -2 1 3 1 109.47 502.08 -#endif - - diff --git a/share/top/encads.ff/ffbonded.itp b/share/top/encads.ff/ffbonded.itp deleted file mode 100644 index 831fd6a3da..0000000000 --- a/share/top/encads.ff/ffbonded.itp +++ /dev/null @@ -1,856 +0,0 @@ -[ bondtypes ] - ; i j func b0 kb - OW HW 1 0.10000 209200.0 - OH HO 1 0.10000 209200.0 - N1 HN 1 0.10000 209200.0 - N2 HN 1 0.10000 209200.0 - C1 H 1 0.10900 209200.0 - C2 H 1 0.10900 209200.0 - C3 H 1 0.10900 209200.0 - CP H 1 0.10900 209200.0 - C1 O 1 0.14370 209200.0 - C2 O2 1 0.14370 209200.0 - C2 OR 1 0.14370 209200.0 - C1 OH 1 0.14390 209200.0 - C2 OH 1 0.14390 209200.0 - C3 OH 1 0.14390 209200.0 - C1 N 1 0.14670 209200.0 - C1 N1 1 0.14670 209200.0 - C1 N2 1 0.14670 209200.0 - C2 N 1 0.14670 209200.0 - C2 N1 1 0.14670 209200.0 - C2 N2 1 0.14670 209200.0 - C3 N 1 0.14670 209200.0 - C3 N1 1 0.14670 209200.0 - C3 N2 1 0.14670 209200.0 - CP N 1 0.14670 209200.0 - CP N1 1 0.14670 209200.0 - CP N2 1 0.14670 209200.0 - C1 M1 1 0.14720 209200.0 - C1 M2 1 0.14720 209200.0 - C1 M3 1 0.14720 209200.0 - C2 M1 1 0.14720 209200.0 - C2 M2 1 0.14720 209200.0 - C2 M3 1 0.14720 209200.0 - C3 M1 1 0.14720 209200.0 - C3 M2 1 0.14720 209200.0 - C3 M3 1 0.14720 209200.0 - C1 C1 1 0.15250 209200.0 - C1 C2 1 0.15250 209200.0 - C1 C3 1 0.15250 209200.0 - C2 C2 1 0.15250 209200.0 - C2 C3 1 0.15250 209200.0 - C3 C3 1 0.15250 209200.0 - CP CP 1 0.15190 209200.0 - C1 CP 1 0.14980 209200.0 - A6 H 1 0.10900 209200.0 - A5 H 1 0.10900 209200.0 - A7 H 1 0.10900 209200.0 - A6 C1 1 0.15260 209200.0 - A6 C2 1 0.15260 209200.0 - A6 C3 1 0.15260 209200.0 - A6 OH 1 0.13780 209200.0 - A7 C1 1 0.15260 209200.0 - A7 C2 1 0.15260 209200.0 - A7 C3 1 0.15260 209200.0 - Aprime C1 1 0.15260 209200.0 - Abis C1 1 0.15260 209200.0 - Aprime C2 1 0.15260 209200.0 - Aprime C3 1 0.15260 209200.0 - Abis C2 1 0.15260 209200.0 - Abis C3 1 0.15260 209200.0 - Aprime O 1 0.12360 418400.0 - Aprime OH 1 0.12360 418400.0 - Abis Obis 1 0.12230 418400.0 - Aprime N 1 0.13220 418400.0 - Aprime N1 1 0.13220 418400.0 - Aprime N2 1 0.13220 418400.0 - A5 N 1 0.13340 418400.0 - A5 N1 1 0.13340 418400.0 - A5 N2 1 0.13340 418400.0 - A5 C1 1 0.15160 209200.0 - A5 C2 1 0.15160 209200.0 - A5 C3 1 0.15160 209200.0 - A5 A5 1 0.13760 418400.0 - A5 A7 1 0.14510 418400.0 - A5 L5 1 0.13340 418400.0 - A6 O 1 0.12280 418400.0 - A6 O2 1 0.12280 418400.0 - A6 OR 1 0.12280 418400.0 - A6 A6 1 0.13890 418400.0 - A6 A7 1 0.14110 418400.0 - A6 M1 1 0.13350 418400.0 - A6 M2 1 0.13350 418400.0 - A6 M3 1 0.13350 418400.0 - A7 N 1 0.13670 418400.0 - A7 N2 1 0.13670 418400.0 - A7 N1 1 0.13430 418400.0 - A7 A7 1 0.13640 418400.0 - SH H 1 0.13300 209200.0 - S C2 1 0.18080 209200.0 - S C3 1 0.18080 209200.0 - SH C2 1 0.18080 209200.0 - S S 1 0.20150 209200.0 - M1 HN 1 0.10000 209200.0 - M2 HN 1 0.10000 209200.0 - M3 HN 1 0.10000 209200.0 - A6 N 1 0.13550 418400.0 - A6 N1 1 0.13550 418400.0 - A6 N2 1 0.13550 418400.0 - A6 L5 1 0.13550 418400.0 - A6 L6 1 0.13550 418400.0 - A7 L5 1 0.13670 418400.0 - A7 L6 1 0.13670 418400.0 - P OP 1 0.14800 418400.0 - P O2 1 0.15940 209200.0 - Y A6 1 0.13960 418400.0 - Y Aprime 1 0.13960 418400.0 - Y R 1 0.13840 418400.0 - Y W 1 0.13840 418400.0 - Z C2 1 0.15170 209200.0 - Z C3 1 0.15170 209200.0 - Z A6 1 0.14900 418400.0 - Z Aprime 1 0.14900 418400.0 - Z Y 1 0.14440 418400.0 - Z Z 1 0.13570 418400.0 - FE N 1 0.19800 58576.0 - FE N1 1 0.19800 58576.0 - FE N2 1 0.19800 58576.0 - FE W 1 0.19800 58576.0 - OF FE 1 0.16320 58576.0 ; iron-oxygen bond - OF OF 1 0.12240 418400.0 - -;[ constrainttypes ] - -[ angletypes ] - ; i j k func th0 cth - HW OW HW 1 109.47 502.08 - C1 OH HO 1 110.00 502.08 - C2 OH HO 1 110.00 502.08 - C3 OH HO 1 110.00 502.08 - Aprime OH HO 1 110.00 502.08 - A6 OH HO 1 110.00 502.08 - C1 C1 Abis 1 110.10 502.08 - C2 C1 Abis 1 110.10 502.08 - C3 C1 Abis 1 110.10 502.08 - HN N2 HN 1 120.00 502.08 - CP N1 HN 1 119.50 502.08 - CP N2 HN 1 119.50 502.08 - C1 N1 HN 1 119.50 502.08 - C1 N2 HN 1 119.50 502.08 - C2 N1 HN 1 119.50 502.08 - C2 N2 HN 1 119.50 502.08 - C3 N1 HN 1 119.50 502.08 - C3 N2 HN 1 119.50 502.08 - A6 N1 HN 1 119.60 502.08 - A6 N2 HN 1 119.60 502.08 - A5 N1 HN 1 119.60 502.08 - A5 N2 HN 1 119.60 502.08 - A7 N1 HN 1 119.60 502.08 - A7 N2 HN 1 119.60 502.08 - Aprime N1 HN 1 119.60 502.08 - Aprime N2 HN 1 119.60 502.08 - N2 Aprime N2 1 113.00 502.08 - C2 Aprime C3 1 118.00 502.08 - C1 N C1 1 112.40 502.08 - C1 N C2 1 112.40 502.08 - C1 N C3 1 112.40 502.08 - C1 N1 CP 1 112.40 502.08 - C1 N1 C1 1 112.40 502.08 - C1 N1 C2 1 112.40 502.08 - C1 N1 C3 1 112.40 502.08 - C1 N2 CP 1 112.40 502.08 - C1 N2 C1 1 112.40 502.08 - C1 N2 C2 1 112.40 502.08 - C1 N2 C3 1 112.40 502.08 - C2 N C2 1 112.40 502.08 - C2 N C3 1 112.40 502.08 - C2 N1 C2 1 112.40 502.08 - C2 N1 C3 1 112.40 502.08 - C2 N2 C2 1 112.40 502.08 - C2 N2 C3 1 112.40 502.08 - C3 N C3 1 112.40 502.08 - C3 N1 C3 1 112.40 502.08 - C3 N2 C3 1 112.40 502.08 - C1 N CP 1 112.40 502.08 - A6 N C1 1 121.30 502.08 - A6 N C2 1 121.30 502.08 - A6 N C3 1 121.30 502.08 - A6 N1 C1 1 121.30 502.08 - A6 N1 C2 1 121.30 502.08 - A6 N1 C3 1 121.30 502.08 - A6 N2 C1 1 121.30 502.08 - A6 N2 C2 1 121.30 502.08 - A6 N2 C3 1 121.30 502.08 - A5 N C1 1 121.30 502.08 - A5 N C2 1 121.30 502.08 - A5 N C3 1 121.30 502.08 - A5 N1 C1 1 121.30 502.08 - A5 N1 C2 1 121.30 502.08 - A5 N1 C3 1 121.30 502.08 - A5 N2 C1 1 121.30 502.08 - A5 N2 C2 1 121.30 502.08 - A5 N2 C3 1 121.30 502.08 - A7 N C1 1 121.30 502.08 - A7 N C2 1 121.30 502.08 - A7 N C3 1 121.30 502.08 - A7 N1 C1 1 121.30 502.08 - A7 N1 C2 1 121.30 502.08 - A7 N1 C3 1 121.30 502.08 - A7 N2 C1 1 121.30 502.08 - A7 N2 C2 1 121.30 502.08 - A7 N2 C3 1 121.30 502.08 - Aprime N C1 1 121.30 502.08 - Aprime N C2 1 121.30 502.08 - Aprime N C3 1 121.30 502.08 - Aprime N1 C1 1 121.30 502.08 - Aprime N1 C2 1 121.30 502.08 - Aprime N1 C3 1 121.30 502.08 - Aprime N2 C1 1 121.30 502.08 - Aprime N2 C2 1 121.30 502.08 - Aprime N2 C3 1 121.30 502.08 - A5 N A5 1 108.00 1004.16 - A5 N1 A5 1 108.00 1004.16 - A5 N2 A5 1 108.00 1004.16 - A5 N1 A7 1 108.00 1004.16 - H C1 H 1 109.50 502.08 - H C2 H 1 109.50 502.08 - H C3 H 1 109.50 502.08 - H CP H 1 109.50 502.08 - O C1 H 1 109.00 502.08 - OH C1 H 1 109.00 502.08 - OH C2 H 1 109.00 502.08 - OH C3 H 1 109.00 502.08 - O2 C2 H 1 109.00 502.08 - OR C2 H 1 109.00 502.08 - O C1 C1 1 109.50 502.08 - O C1 C2 1 109.50 502.08 - O C1 C3 1 109.50 502.08 - OH C1 C1 1 107.90 502.08 - OH C1 C2 1 107.90 502.08 - OH C1 C3 1 107.90 502.08 - OH C2 C1 1 107.90 502.08 - OH C2 C2 1 107.90 502.08 - OH C2 C3 1 107.90 502.08 - O2 C2 C1 1 109.50 502.08 - O2 C2 C2 1 109.50 502.08 - O2 C2 C3 1 109.50 502.08 - OR C2 C1 1 109.50 502.08 - OR C2 C2 1 109.50 502.08 - OR C2 C3 1 109.50 502.08 - C1 C1 H 1 109.50 502.08 - C1 C2 H 1 109.50 502.08 - C1 C3 H 1 109.50 502.08 - C1 CP H 1 109.50 502.08 - C2 C1 H 1 109.50 502.08 - C2 C2 H 1 109.50 502.08 - C2 C3 H 1 109.50 502.08 - C3 C1 H 1 109.50 502.08 - C3 C2 H 1 109.50 502.08 - C3 C3 H 1 109.50 502.08 - CP C1 H 1 109.50 502.08 - CP CP H 1 109.50 502.08 - N C1 H 1 109.50 502.08 - N C2 H 1 109.50 502.08 - N C3 H 1 109.50 502.08 - N CP H 1 109.50 502.08 - N1 CP H 1 109.50 502.08 - N1 C1 H 1 109.50 502.08 - N1 C2 H 1 109.50 502.08 - N1 C3 H 1 109.50 502.08 - N2 CP H 1 109.50 502.08 - N2 C1 H 1 109.50 502.08 - N2 C2 H 1 109.50 502.08 - N2 C3 H 1 109.50 502.08 - M1 C1 H 1 109.50 502.08 - M1 C2 H 1 109.50 502.08 - M1 C3 H 1 109.50 502.08 - M2 C1 H 1 109.50 502.08 - M2 C2 H 1 109.50 502.08 - M2 C3 H 1 109.50 502.08 - M3 C1 H 1 109.50 502.08 - M3 C2 H 1 109.50 502.08 - M3 C3 H 1 109.50 502.08 - M1 C1 C1 1 111.00 502.08 - M1 C1 C2 1 111.00 502.08 - M1 C1 C3 1 111.00 502.08 - M1 C2 C1 1 111.00 502.08 - M1 C2 C2 1 111.00 502.08 - M1 C2 C3 1 111.00 502.08 - M2 C1 C1 1 111.00 502.08 - M2 C1 C2 1 111.00 502.08 - M2 C1 C3 1 111.00 502.08 - M2 C2 C1 1 111.00 502.08 - M2 C2 C2 1 111.00 502.08 - M2 C2 C3 1 111.00 502.08 - M3 C1 C1 1 111.00 502.08 - M3 C1 C2 1 111.00 502.08 - M3 C1 C3 1 111.00 502.08 - M3 C2 C1 1 111.00 502.08 - M3 C2 C2 1 111.00 502.08 - M3 C2 C3 1 111.00 502.08 - A6 C1 H 1 109.50 502.08 - A6 C2 H 1 109.50 502.08 - A6 C3 H 1 109.50 502.08 - A5 C1 H 1 109.50 502.08 - A5 C2 H 1 109.50 502.08 - A5 C3 H 1 109.50 502.08 - A7 C1 H 1 109.50 502.08 - A7 C2 H 1 109.50 502.08 - A7 C3 H 1 109.50 502.08 - Aprime C1 H 1 109.50 502.08 - Aprime C2 H 1 109.50 502.08 - Aprime C3 H 1 109.50 502.08 - Abis C2 H 1 109.50 502.08 - Abis C3 H 1 109.50 502.08 - Abis C1 H 1 109.50 502.08 - C1 C1 N 1 109.10 502.08 - C1 C1 N1 1 109.10 502.08 - C1 C1 N2 1 109.10 502.08 - C1 C2 N 1 109.10 502.08 - C1 C2 N1 1 109.10 502.08 - C1 C2 N2 1 109.10 502.08 - C2 C1 N 1 109.10 502.08 - C2 C1 N1 1 109.10 502.08 - C2 C1 N2 1 109.10 502.08 - C2 C2 N 1 109.10 502.08 - C2 C2 N1 1 109.10 502.08 - C2 C2 N2 1 109.10 502.08 - C3 C1 N 1 109.10 502.08 - C3 C1 N1 1 109.10 502.08 - C3 C1 N2 1 109.10 502.08 - C3 C2 N 1 109.10 502.08 - C3 C2 N1 1 109.10 502.08 - C3 C2 N2 1 109.10 502.08 - CP C1 N 1 104.00 502.08 - CP C1 N1 1 109.10 502.08 - CP C1 N2 1 109.10 502.08 - A6 C1 N 1 111.30 502.08 - A6 C1 N1 1 111.30 502.08 - A6 C1 N2 1 111.30 502.08 - A6 C2 N 1 111.30 502.08 - A6 C2 N1 1 111.30 502.08 - A6 C2 N2 1 111.30 502.08 - A5 C1 N 1 111.30 502.08 - A5 C1 N1 1 111.30 502.08 - A5 C1 N2 1 111.30 502.08 - A5 C2 N 1 111.30 502.08 - A5 C2 N1 1 111.30 502.08 - A5 C2 N2 1 111.30 502.08 - A7 C1 N 1 111.30 502.08 - A7 C1 N1 1 111.30 502.08 - A7 C1 N2 1 111.30 502.08 - A7 C2 N 1 111.30 502.08 - A7 C2 N1 1 111.30 502.08 - A7 C2 N2 1 111.30 502.08 - Aprime C1 N 1 111.30 502.08 - Aprime C1 N1 1 111.30 502.08 - Aprime C1 N2 1 111.30 502.08 - Aprime C2 N 1 111.30 502.08 - Aprime C2 N1 1 111.30 502.08 - Aprime C2 N2 1 111.30 502.08 - Abis C2 N 1 111.30 502.08 - Abis C2 N1 1 111.30 502.08 - Abis C2 N2 1 111.30 502.08 - A6 C1 M1 1 111.30 502.08 - A6 C1 M2 1 111.30 502.08 - A6 C1 M3 1 111.30 502.08 - A6 C2 M1 1 111.30 502.08 - A6 C2 M2 1 111.30 502.08 - A6 C2 M3 1 111.30 502.08 - A5 C1 M1 1 111.30 502.08 - A5 C1 M2 1 111.30 502.08 - A5 C1 M3 1 111.30 502.08 - A5 C2 M1 1 111.30 502.08 - A5 C2 M2 1 111.30 502.08 - A5 C2 M3 1 111.30 502.08 - A7 C1 M1 1 111.30 502.08 - A7 C1 M2 1 111.30 502.08 - A7 C1 M3 1 111.30 502.08 - A7 C2 M1 1 111.30 502.08 - A7 C2 M2 1 111.30 502.08 - A7 C2 M3 1 111.30 502.08 - Aprime C1 M1 1 111.30 502.08 - Aprime C1 M2 1 111.30 502.08 - Aprime C1 M3 1 111.30 502.08 - Aprime C2 M1 1 111.30 502.08 - Aprime C2 M2 1 111.30 502.08 - Aprime C2 M3 1 111.30 502.08 - Abis C2 M1 1 111.30 502.08 - Abis C2 M2 1 111.30 502.08 - Abis C2 M3 1 111.30 502.08 - Abis C1 M1 1 111.30 502.08 - Abis C1 M2 1 111.30 502.08 - Abis C1 M3 1 111.30 502.08 - Abis C1 N 1 111.30 502.08 - Abis C1 N1 1 111.30 502.08 - Abis C1 N2 1 111.30 502.08 - C1 C1 C1 1 111.40 502.08 - C1 C1 C2 1 111.40 502.08 - C1 C1 C3 1 111.40 502.08 - C1 C2 C1 1 111.40 502.08 - C1 C2 C2 1 111.40 502.08 - C1 C2 C3 1 111.40 502.08 - C1 CP CP 1 107.20 502.08 - C2 C1 C2 1 111.40 502.08 - C2 C1 C3 1 111.40 502.08 - C2 C2 C2 1 111.40 502.08 - C2 C2 C3 1 111.40 502.08 - C3 C1 C3 1 111.40 502.08 - C3 C2 C3 1 111.40 502.08 - CP CP CP 1 103.90 502.08 - N CP CP 1 105.10 502.08 - N1 CP CP 1 105.10 502.08 - N2 CP CP 1 105.10 502.08 - Aprime N CP 1 125.80 502.08 - A6 C1 C1 1 114.10 502.08 - A6 C1 C2 1 114.10 502.08 - A6 C1 C3 1 114.10 502.08 - A6 C2 C1 1 114.10 502.08 - A6 C2 C2 1 114.10 502.08 - A6 C2 C3 1 114.10 502.08 - A5 C1 C1 1 113.90 502.08 - A5 C1 C2 1 113.90 502.08 - A5 C1 C3 1 113.90 502.08 - A5 C2 C1 1 113.90 502.08 - A5 C2 C2 1 113.90 502.08 - A5 C2 C3 1 113.90 502.08 - A7 C1 C1 1 110.10 502.08 - A7 C1 C2 1 110.10 502.08 - A7 C1 C3 1 110.10 502.08 - A7 C2 C1 1 110.10 502.08 - A7 C2 C2 1 110.10 502.08 - A7 C2 C3 1 110.10 502.08 - Aprime C1 C1 1 110.10 502.08 - Aprime C1 C2 1 110.10 502.08 - Aprime C1 C3 1 110.10 502.08 - Aprime C1 CP 1 111.90 502.08 - Abis C1 CP 1 110.10 502.08 - Aprime C2 C1 1 110.10 502.08 - Aprime C2 C2 1 110.10 502.08 - Aprime C2 C3 1 110.10 502.08 - Abis C2 C1 1 110.10 502.08 - Abis C2 C2 1 110.10 502.08 - Abis C2 C3 1 110.10 502.08 - S C2 C1 1 115.50 502.08 - S C2 C2 1 115.50 502.08 - S C2 C3 1 115.50 502.08 - SH C2 C1 1 115.50 502.08 - SH C2 C2 1 115.50 502.08 - SH C2 C3 1 115.50 502.08 - S C2 H 1 110.00 502.08 - S C3 H 1 110.00 502.08 - SH C2 H 1 110.00 502.08 - C2 SH H 1 110.00 502.08 - H A6 H 1 120.00 502.08 - H A5 H 1 120.00 502.08 - H A7 H 1 120.00 502.08 - A6 A6 H 1 120.00 502.08 - A6 A7 H 1 120.00 502.08 - A5 A5 H 1 126.00 502.08 - A5 A7 H 1 120.00 502.08 - A7 A6 H 1 120.00 502.08 - A7 A5 H 1 126.00 502.08 - A7 A7 H 1 120.00 502.08 - O A6 O 1 120.00 502.08 - O Aprime O 1 120.00 502.08 - OH Aprime O 1 120.00 502.08 - O2 A6 O 1 120.00 502.08 - OR A6 O 1 120.00 502.08 - N A6 H 1 120.00 502.08 - N A5 H 1 126.00 502.08 - N A7 H 1 120.00 502.08 - N1 A6 H 1 120.00 502.08 - N1 A5 H 1 126.00 502.08 - N1 A7 H 1 120.00 502.08 - N2 A6 H 1 120.00 502.08 - N2 A5 H 1 126.00 502.08 - N2 A7 H 1 120.00 502.08 - N Aprime O 1 123.50 1004.16 - N1 Aprime O 1 123.50 1004.16 - N2 Aprime O 1 123.50 1004.16 - C1 Aprime O 1 121.00 502.08 - C1 Aprime OH 1 121.00 502.08 - C2 Aprime O 1 121.00 502.08 - C2 Aprime OH 1 121.00 502.08 - C3 Aprime O 1 121.00 502.08 - C3 Aprime C3 1 121.00 502.08 - C1 Aprime N 1 115.50 502.08 - C1 Aprime N1 1 115.50 502.08 - C1 Aprime N2 1 115.50 502.08 - C2 Aprime N 1 115.50 502.08 - C2 Aprime N1 1 115.50 502.08 - C2 Aprime N2 1 115.50 502.08 - C3 Aprime N 1 115.50 502.08 - C3 Aprime N1 1 115.50 502.08 - C3 Aprime N2 1 115.50 502.08 - Obis Abis C1 1 117.70 502.08 - Obis Abis C2 1 117.70 502.08 - Obis Abis C3 1 117.70 502.08 - Obis Abis Obis 1 124.60 1004.16 - C2 A5 A5 1 126.00 502.08 - C2 A5 L5 1 126.00 502.08 - L5 A5 H 1 126.00 502.08 - C2 A5 A7 1 126.00 502.08 - A5 A5 N 1 108.00 1004.16 - A5 A5 N1 1 108.00 1004.16 - A5 A5 N2 1 108.00 1004.16 - A5 A5 L5 1 108.00 1004.16 - N1 A5 L5 1 108.00 1004.16 - C2 A5 N1 1 126.00 502.08 - A7 A5 A5 1 108.00 1004.16 - M1 A6 M1 1 120.00 1004.16 - M1 A6 M2 1 120.00 1004.16 - M1 A6 M3 1 120.00 1004.16 - M2 A6 M2 1 120.00 1004.16 - M2 A6 M3 1 120.00 1004.16 - M3 A6 M3 1 120.00 1004.16 - A6 A6 C1 1 120.10 502.08 - A6 A6 C2 1 120.10 502.08 - A6 A6 C3 1 120.10 502.08 - A6 A6 A6 1 120.00 1004.16 - A6 A6 OH 1 118.40 502.08 - A7 A6 A6 1 120.00 1004.16 - A5 A7 A7 1 108.00 1004.16 - A7 A7 A6 1 120.00 1004.16 - A5 A7 A6 1 132.00 1004.16 - N A7 A6 1 132.00 502.08 - N1 A7 A6 1 132.00 502.08 - N2 A7 A6 1 132.00 502.08 - N1 A7 A7 1 108.00 1004.16 - L5 A7 A6 1 132.00 502.08 - L6 A7 A6 1 132.00 502.08 - C2 S C2 1 99.10 502.08 - C2 S C3 1 99.10 502.08 - S S C2 1 104.30 502.08 - HN M2 HN 1 120.00 502.08 - HN M3 HN 1 109.50 502.08 - C1 M1 HN 1 119.50 502.08 - C1 M2 HN 1 119.50 502.08 - C1 M3 HN 1 109.50 502.08 - C2 M1 HN 1 119.50 502.08 - C2 M2 HN 1 119.50 502.08 - C2 M3 HN 1 109.50 502.08 - C3 M1 HN 1 119.50 502.08 - C3 M2 HN 1 119.50 502.08 - C3 M3 HN 1 109.50 502.08 - A6 M1 HN 1 119.60 502.08 - A6 M2 HN 1 119.60 502.08 - A6 M3 HN 1 119.60 502.08 - A6 M1 C1 1 123.20 502.08 - A6 M1 C2 1 123.20 502.08 - A6 M1 C3 1 123.20 502.08 - A6 M2 C1 1 123.20 502.08 - A6 M2 C2 1 123.20 502.08 - A6 M2 C3 1 123.20 502.08 - A6 M3 C1 1 123.20 502.08 - A6 M3 C2 1 123.20 502.08 - A6 M3 C3 1 123.20 502.08 - A5 L5 A5 1 108.00 1004.16 - A6 N1 A6 1 120.00 502.08 - OH C1 N 1 109.50 502.08 - OH C1 N1 1 109.50 502.08 - OH C1 N2 1 109.50 502.08 - C3 A7 A6 1 108.86 502.08 - C3 A7 A7 1 132.53 502.08 - L5 A7 A7 1 108.00 502.08 - A7 A7 L6 1 120.00 502.08 - A5 L5 A7 1 108.00 502.08 - A6 L5 A7 1 119.33 502.08 - N1 A5 N1 1 108.00 1004.16 - Y A6 H 1 120.00 502.08 - Z C2 H 1 110.00 502.08 - Z C3 H 1 110.00 502.08 - Z A6 H 1 120.00 502.08 - A6 N FE 1 120.00 502.08 - A6 N1 FE 1 120.00 502.08 - A6 N2 FE 1 120.00 502.08 - A5 N FE 1 120.00 502.08 - A5 N1 FE 1 120.00 502.08 - A5 N2 FE 1 120.00 502.08 - A7 N FE 1 120.00 502.08 - A7 N1 FE 1 120.00 502.08 - A7 N2 FE 1 120.00 502.08 - Aprime N FE 1 120.00 502.08 - Aprime N1 FE 1 120.00 502.08 - Aprime N2 FE 1 120.00 502.08 - Y R Y 1 105.40 1004.16 - Y A6 Y 1 124.50 502.08 - Y Aprime Y 1 124.50 502.08 - Y W Y 1 105.40 502.08 - FE W Y 1 127.30 502.08 - R Y A6 1 125.50 1004.16 - R Y Aprime 1 125.50 1004.16 - W Y A6 1 125.20 1004.16 - W Y Aprime 1 125.20 1004.16 - Z Y A6 1 124.20 1004.16 - Z Y Aprime 1 124.20 1004.16 - Z Y R 1 109.50 1004.16 - Z Y W 1 109.50 1004.16 - Y Z C2 1 125.40 502.08 - Y Z C3 1 125.40 502.08 - Y Z A6 1 124.40 1004.16 - Y Z Aprime 1 124.40 1004.16 - Z Z C2 1 127.50 502.08 - Z Z C3 1 127.50 502.08 - Z Z A6 1 128.40 1004.16 - Z Z Aprime 1 128.40 1004.16 - Z Z Y 1 107.00 1004.16 - Z C2 C1 1 109.50 502.08 - Z C2 C2 1 109.50 502.08 - Z C2 C3 1 109.50 502.08 - Z A6 A6 1 120.00 1004.16 - Z A6 A7 1 120.00 1004.16 - W FE N 1 90.00 502.08 - W FE N1 1 90.00 502.08 - W FE N2 1 90.00 502.08 - W FE W 1 180.00 502.08 - OF FE N 1 180.00 502.08 - OF FE N1 1 180.00 502.08 - OF FE N2 1 180.00 502.08 - OF FE W 1 90.00 502.08 - OF OF FE 1 120.00 502.08 - - -[ dihedraltypes ] -; Encad proper dihedrals. Note that there is a difference pf -; sign in the cosine definition between Gromacs and Encad. All angle values -; here are thus offset 180 degrees. - ; i l func q0 cq - C1 A6 A6 H 1 180.00 167.36 1 - C2 A6 A6 H 1 180.00 167.36 1 - C2 A5 A5 H 1 180.00 167.36 1 - C2 A5 A7 H 1 180.00 167.36 1 - C3 A6 A6 H 1 180.00 167.36 1 - C3 A7 A6 H 1 180.00 167.36 1 - C3 A7 A7 H 1 180.00 167.36 1 - C2 A5 A7 A6 1 180.00 167.36 1 - H A6 N C1 1 180.00 167.36 1 - A6 A6 A6 H 1 0.00 167.36 1 - L5 A7 A7 L5 1 0.00 167.36 1 - L5 A7 A7 L6 1 0.00 167.36 1 - L6 A7 A7 L6 1 0.00 167.36 1 - N A7 A6 A6 1 0.00 167.36 1 - N1 A7 A6 A6 1 0.00 167.36 1 - N2 A7 A6 A6 1 0.00 167.36 1 - N1 A7 A7 A6 1 0.00 167.36 1 - A6 A7 L5 A5 1 180.00 83.68 2 - A7 A7 N1 A5 1 180.00 167.36 1 - Aprime N C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N1 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N1 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N2 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N2 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp - HN N2 Aprime N2 1 180.00 41.84 2 ; not present in aanahn - C1 Aprime N C1 1 180.00 41.84 2 - C1 Aprime N C2 1 180.00 41.84 2 - C1 Aprime N C3 1 180.00 41.84 2 - C1 Aprime N1 C1 1 180.00 41.84 2 - C1 Aprime N1 C2 1 180.00 41.84 2 - C1 Aprime N1 C3 1 180.00 41.84 2 - C1 Aprime N2 C1 1 180.00 41.84 2 - C1 Aprime N2 C2 1 180.00 41.84 2 - C1 Aprime N2 C3 1 180.00 41.84 2 - C2 Aprime N C1 1 180.00 41.84 2 - C2 Aprime N C2 1 180.00 41.84 2 - C2 Aprime N C3 1 180.00 41.84 2 - C2 Aprime N1 C1 1 180.00 41.84 2 - C2 Aprime N1 C2 1 180.00 41.84 2 - C2 Aprime N1 C3 1 180.00 41.84 2 - C2 Aprime N2 C1 1 180.00 41.84 2 - C2 Aprime N2 C2 1 180.00 41.84 2 - C2 Aprime N2 C3 1 180.00 41.84 2 - C3 Aprime N C1 1 180.00 41.84 2 - C3 Aprime N C2 1 180.00 41.84 2 - C3 Aprime N C3 1 180.00 41.84 2 - C3 Aprime N1 C1 1 180.00 41.84 2 - C3 Aprime N1 C2 1 180.00 41.84 2 - C3 Aprime N1 C3 1 180.00 41.84 2 - C3 Aprime N2 C1 1 180.00 41.84 2 - C3 Aprime N2 C2 1 180.00 41.84 2 - C3 Aprime N2 C3 1 180.00 41.84 2 - C1 Aprime N1 HN 1 180.00 41.84 2 - C1 Aprime N2 HN 1 180.00 41.84 2 - C2 Aprime N1 HN 1 180.00 41.84 2 - C2 Aprime N2 HN 1 180.00 41.84 2 - C3 Aprime N1 HN 1 180.00 41.84 2 - C3 Aprime N2 HN 1 180.00 41.84 2 - C1 A6 A6 A6 1 0.00 334.72 1 - C2 A6 A6 A6 1 0.00 334.72 1 - C3 A6 A6 A6 1 0.00 334.72 1 - A6 A6 A6 A6 1 180.00 334.72 1 - N C1 CP CP 1 180.00 41.84 1 - N1 C1 CP CP 1 180.00 41.84 1 - N2 C1 CP CP 1 180.00 41.84 1 - C1 Aprime N CP 1 180.00 41.84 2 - C2 Aprime N CP 1 180.00 41.84 2 - C3 Aprime N CP 1 180.00 41.84 2 - Aprime N CP CP 1 0.00 41.84 1 - C1 A6 A6 X 1 180.00 41.84 2 - C2 A6 A6 X 1 180.00 41.84 2 - C2 A5 A5 X 1 180.00 41.84 2 - C2 A5 A7 X 1 180.00 41.84 2 - C3 A6 A6 X 1 180.00 41.84 2 - C3 A7 A6 X 1 180.00 41.84 2 - C3 A7 A7 X 1 180.00 41.84 2 - X A5 N C1 1 0.00 167.36 1 - X A5 N C2 1 0.00 167.36 1 - X A5 N C3 1 0.00 167.36 1 - X A5 N1 C1 1 0.00 167.36 1 - X A5 N1 C2 1 0.00 167.36 1 - X A5 N1 C3 1 0.00 167.36 1 - X A5 N2 C1 1 0.00 167.36 1 - X A5 N2 C2 1 0.00 167.36 1 - X A5 N2 C3 1 0.00 167.36 1 - C2 A5 N1 X 1 0.00 167.36 1 - X A6 N C1 1 0.00 167.36 1 - X A6 N C2 1 0.00 167.36 1 - X A6 N C3 1 0.00 167.36 1 - X A7 N C1 1 180.00 167.36 1 - X A7 N C2 1 180.00 167.36 1 - X A7 N C3 1 180.00 167.36 1 - X A7 N1 C1 1 180.00 167.36 1 - X A7 N1 C2 1 180.00 167.36 1 - X A7 N1 C3 1 180.00 167.36 1 - X A7 N2 C1 1 180.00 167.36 1 - X A7 N2 C2 1 180.00 167.36 1 - X A7 N2 C3 1 180.00 167.36 1 - S S C2 X 1 0.00 0.00 0 ; will be removed by grompp - X A6 A6 X 1 180.00 167.36 1 - X A6 A7 X 1 180.00 167.36 1 - X A5 A5 X 1 180.00 167.36 1 - X A5 A7 X 1 180.00 167.36 1 - X A7 A7 X 1 180.00 167.36 1 - X A5 N X 1 180.00 334.72 2 - X A5 N1 X 1 180.00 334.72 2 - X A5 N2 X 1 180.00 334.72 2 - X A5 L5 X 1 180.00 41.84 2 - X A6 N X 1 180.00 167.36 1 - X A6 N1 X 1 180.00 167.36 1 - X A6 N2 X 1 180.00 167.36 1 - X A6 L5 X 1 180.00 167.36 1 - X A6 L6 X 1 180.00 167.36 1 - X A7 L5 X 1 180.00 167.36 1 - X A7 L6 X 1 180.00 167.36 1 - X P O2 X 1 0.00 8.368 3 - X P OP X 1 0.00 8.368 3 - X N C1 X 1 0.00 0.00 0 ; will be removed by grompp - X N C2 X 1 0.00 0.00 0 ; will be removed by grompp - X N C3 X 1 0.00 0.00 0 ; will be removed by grompp - X N CP X 1 0.00 0.00 0 ; will be removed by grompp - X N1 C1 X 1 0.00 0.00 0 ; will be removed by grompp - X N1 C2 X 1 0.00 0.00 0 ; will be removed by grompp - X N1 C3 X 1 0.00 0.00 0 ; will be removed by grompp - X N1 CP X 1 0.00 0.00 0 ; will be removed by grompp - X N2 C1 X 1 0.00 0.00 0 ; will be removed by grompp - X N2 C2 X 1 0.00 0.00 0 ; will be removed by grompp - X N2 C3 X 1 0.00 0.00 0 ; will be removed by grompp - X N2 CP X 1 0.00 0.00 0 ; will be removed by grompp - X C1 O X 1 0.00 2.5104 3 - X C1 OH X 1 0.00 2.5104 3 - X C2 OH X 1 0.00 2.5104 3 - X C2 O2 X 1 0.00 2.5104 3 - X C2 OR X 1 0.00 2.5104 3 - X C3 OH X 1 0.00 2.5104 3 - X C1 C1 X 1 0.00 5.8576 3 - X C1 C2 X 1 0.00 5.8576 3 - X C1 C3 X 1 0.00 5.8576 3 - X C2 C2 X 1 0.00 5.8576 3 - X C2 C3 X 1 0.00 5.8576 3 - X C3 C3 X 1 0.00 5.8576 3 - X C1 CP X 1 180.00 5.8576 3 - X CP CP X 1 180.00 5.8576 3 - X C1 Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X C2 Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X C3 Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X CP Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X C1 A6 X 1 0.00 0.4184 6 - X C1 A5 X 1 0.00 0.4184 6 - X C1 A7 X 1 0.00 0.4184 6 - X C1 Abis X 1 0.00 0.4184 6 - X C2 A6 X 1 0.00 0.4184 6 - X C2 A5 X 1 0.00 0.4184 6 - X C2 A7 X 1 0.00 0.4184 6 - X C2 Abis X 1 0.00 0.4184 6 - X C3 A6 X 1 0.00 0.4184 6 - X C3 A5 X 1 0.00 0.4184 6 - X C3 A7 X 1 0.00 0.4184 6 - X C3 Abis X 1 0.00 0.4184 6 - X C1 M3 X 1 0.00 5.8576 3 - X C2 M3 X 1 0.00 5.8576 3 - X C3 M3 X 1 0.00 5.8576 3 - X A6 O2 X 1 0.00 2.5104 3 - X Aprime OH X 1 0.00 2.5104 3 - X A6 OH X 1 0.00 2.5104 3 - X A6 M1 X 1 180.00 41.84 2 - X A6 M2 X 1 180.00 41.84 2 - X A6 M3 X 1 180.00 41.84 2 - X S C2 X 1 0.00 4.184 3 - X S C3 X 1 0.00 4.184 3 - X SH C2 X 1 0.00 4.184 3 - X S S X 1 0.00 25.104 2 - X M1 C1 X 1 0.00 5.8576 3 - X M1 C2 X 1 0.00 5.8576 3 - X M1 C3 X 1 0.00 5.8576 3 - X M2 C1 X 1 0.00 5.8576 3 - X M2 C2 X 1 0.00 5.8576 3 - X M2 C3 X 1 0.00 5.8576 3 - X Y A6 X 1 180.00 41.84 2 - X Y Aprime X 1 180.00 41.84 2 - X Y R X 1 180.00 83.68 2 - X Y W X 1 180.00 83.68 2 - X Z C2 X 1 0.00 0.4184 6 - X Z C3 X 1 0.00 0.4184 6 - X Z A6 X 1 180.00 41.84 2 - X Z Aprime X 1 180.00 41.84 2 - X Z Y X 1 180.00 83.68 2 - X Z Z X 1 180.00 83.68 2 - X FE N X 1 0.00 0.00 0 ; will be removed by grompp - X FE N1 X 1 0.00 0.00 0 ; will be removed by grompp - X FE N2 X 1 0.00 0.00 0 ; will be removed by grompp - X FE W X 1 0.00 0.00 0 ; will be removed by grompp - X OF FE X 1 0.00 0.00 0 ; will be removed by grompp - - - -; Encad out-of-plane potentials are the same functional form as -; Gromacs proper dihedrals (i.e. cosine, but with shifted sign). -; Note that the atom order is different too; In Gromacs, the first atom -; of an improper is the center one, while it is the 3rd in Encad. - -; Since they use the same type as proper dihedrals we use defines here -; to avoid mistakes in ambiguous cases. -; -; Note: the three parameters are repeated, to avoid having the free energy B state -; picked up from the default proper dihedral parameter types -; (grompp would give errors about non-matching multiplicity between A/B states) -; -; DNA -#define improper_X_X_P_X 180.0 8.368 3 180.0 8.368 3 -#define improper_X_X_M2_X 180.0 8.368 2 180.0 8.368 2 -; Proteins -#define improper_X_X_N_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_C_X 180.0 8.368 3 180.0 8.368 3 -#define improper_X_X_A_X 180.0 8.368 2 180.0 8.368 2 -#define improper_A_X_C1_X 60.0 75.312 1 60.0 75.312 1 -#define improper_A_X_C1_H -60.0 75.312 1 -60.0 75.312 1 -#define improper_X_X_C1_A 60.0 75.312 1 60.0 75.312 1 -#define improper_C3_C2_C1_C3 60.0 75.312 1 60.0 75.312 1 -#define improper_C_C1_C1_C3 60.0 75.312 1 60.0 75.312 1 -#define improper_C3_C1_C1_OH -60.0 75.312 1 -60.0 75.312 1 -#define improper_C1_C2_C1_C3 -60.0 75.312 1 -60.0 75.312 1 -#define improper_N_A_C1_C -60.0 75.312 1 -60.0 75.312 1 -#define improper_M_A_C1_C -60.0 75.312 1 -60.0 75.312 1 -#define improper_X_X_M_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_M3_X 180.0 8.368 3 180.0 8.368 3 -; Heme -#define improper_X_X_R_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_W_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_Y_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_Z_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_FE_X 180.0 0.000 4 180.0 0.000 4 -#define improper_X_X_OF_X 180.0 8.368 2 180.0 8.368 2 - - - diff --git a/share/top/encads.ff/ffnonbonded.itp b/share/top/encads.ff/ffnonbonded.itp deleted file mode 100644 index 4081f3eae8..0000000000 --- a/share/top/encads.ff/ffnonbonded.itp +++ /dev/null @@ -1,55 +0,0 @@ -[ atomtypes ] -;name at.num mass charge ptype sigma epsilon - H 1 1.008 0.0 A 2.54129e-01 1.58992e-01 - O 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - N 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - N1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - N2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - C1 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - C2 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - C3 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - CP 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - A6 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - A5 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - A7 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - Aprime 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - Abis 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - L5 7 14.0027 0.0 A 2.76223e-01 7.73161e-01 - L6 7 14.0027 0.0 A 2.76223e-01 7.73161e-01 - P 15 30.9738 0.0 A 3.84423e-01 3.08863e-01 - OH 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - O2 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - OR 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - S 16 32.060 0.0 A 3.84423e-01 3.08863e-01 - SH 16 32.060 0.0 A 3.84423e-01 3.08863e-01 - M1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - M2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - M3 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - HN 1 1.008 0.0 A 4.45449e-02 4.18400e-02 - HO 1 1.008 0.0 A 4.45449e-02 4.18400e-02 - HW 1 1.008 0.0 A 4.45449e-02 4.18400e-02 - CL 17 35.453 0.0 A 4.31068e-01 3.51456e-01 - Obis 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - OP 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - R 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - W 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - Y 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - Z 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - FE 26 55.847 0.0 A 3.84423e-01 3.08863e-01 - OF 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - OW 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - AR 18 39.948 0.0 A 2.54129e-01 1.58992e-01 - NA 11 22.9898 0.0 A 2.40543e-01 7.73161e-01 - MCH3 0 0.0 0.0 A 0.0 0.0 - MNH3 0 0.0 0.0 A 0.0 0.0 - MW 0 0.0 0.0 D 0.0 0.0 - -[ nonbond_params ] - ; i j func c6 c12 -; Encad uses strict combination rules, so no need for explicit parameters - -[ pairtypes ] - ; i j func cs6 cs12 -; 1,4 interactions are calculated automatically, using fudge factors. -; (In the current version, the factors are 0.0, meaning no 1,4 interactions). - diff --git a/share/top/encads.ff/forcefield.doc b/share/top/encads.ff/forcefield.doc deleted file mode 100644 index 35c5b999a3..0000000000 --- a/share/top/encads.ff/forcefield.doc +++ /dev/null @@ -1 +0,0 @@ -[DEPRECATED] Encad all-atom force field, using full solvent charges diff --git a/share/top/encads.ff/forcefield.itp b/share/top/encads.ff/forcefield.itp deleted file mode 100644 index bfcbe0b23a..0000000000 --- a/share/top/encads.ff/forcefield.itp +++ /dev/null @@ -1,19 +0,0 @@ -#define _FF_ENCAD -; Implemented from encad library version 25/xi/91, -; with 1,4 interaction setup modified by Michael Levitt. -; In this forcefield, both coulombic and Lennard-Jones interactions -; are completely excluded for 1,4 interaction sites. -; -; Vacuum version - scaled down charges. - -; -[ defaults ] -; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ - 1 3 yes 0.0 0.0 - -#include "ffnonbonded.itp" -#include "ffbonded.itp" - - - - diff --git a/share/top/encads.ff/watermodels.dat b/share/top/encads.ff/watermodels.dat deleted file mode 100644 index 592e150e5f..0000000000 --- a/share/top/encads.ff/watermodels.dat +++ /dev/null @@ -1 +0,0 @@ -f3c F3C flexible three-centered water model diff --git a/share/top/encadv.ff/aminoacids.c.tdb b/share/top/encadv.ff/aminoacids.c.tdb deleted file mode 100644 index 918adc33c6..0000000000 --- a/share/top/encadv.ff/aminoacids.c.tdb +++ /dev/null @@ -1,31 +0,0 @@ -[ None ] - -[ COO- ] -[ replace ] -C C Abis 12.011 0.64 -O O1 Obis 15.9994 -0.42 -OXT O2 Obis 15.9994 -0.42 -[ add ] -2 8 O C CA N - Obis 15.9994 -0.92 -[ dihedrals ] -N CA C O2 -[ impropers ] -CA O2 C O1 improper_X_X_A_X -N C CA CB improper_X_X_C_X - -[ COOH ] -[ replace ] -C C Aprime 12.011 0.38 -O O OH 15.9994 -0.38 -OXT OT O 15.9994 -0.433 -[ add ] -1 2 OT C CA N - O 15.9994 -0.433 -1 2 HO O C CA - HO 1.008 0.433 -[ dihedrals ] -N CA C O -[ impropers ] -OT CA C O improper_X_X_A_X - diff --git a/share/top/encadv.ff/aminoacids.hdb b/share/top/encadv.ff/aminoacids.hdb deleted file mode 100644 index 06e00b703f..0000000000 --- a/share/top/encadv.ff/aminoacids.hdb +++ /dev/null @@ -1,189 +0,0 @@ -ACE 1 -3 4 HH3 CH3 C O -ALA 3 -1 1 H N -C CA -1 5 HA CA N C CB -3 4 HB CB CA N -ARG 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD NE CG -1 1 HE NE CD CZ -2 3 HH1 NH1 CZ NE -2 3 HH2 NH2 CZ NE -ARGN 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD NE CG -1 1 HE NE CD CZ -1 2 HH1 NH1 CZ NE -2 3 HH2 NH2 CZ NE -ASN 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 3 HD2 ND2 CG CB -ASP 3 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -ASPH 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 2 HD2 OD2 CG CB -CYS2 3 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB SG CA -CYSH 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB SG CA -1 2 HG SG CB CA -GLN 5 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 3 HE2 NE2 CD CG -GLU 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -GLUH 5 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -1 2 HE2 OE2 CD CG -GLY 2 -1 1 H N -C CA -2 6 HA CA C N -HIS1 6 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -1 1 HD1 ND1 CG CE1 -HISA 6 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -1 1 HD1 ND1 CG CE1 -HISB 6 -1 1 H N -C CA -2 6 HB CB CG CA -1 5 HA CA N C CB -1 1 HE2 NE2 CE1 CD2 -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -HISH 7 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD2 CD2 CG NE2 -1 1 HE1 CE1 ND1 NE2 -1 1 HD1 ND1 CG CE1 -1 1 HE2 NE2 CE1 CD2 -HOH 1 -2 7 HW OW -ILE 6 -1 1 H N -C CA -1 5 HA CA N C CB -1 5 HB CB CA CG1 CG2 -2 6 HG1 CG1 CD CB -3 4 HG2 CG2 CB CA -3 4 HD CD CG1 CB -LEU 6 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 5 HG CG CB CD1 CD2 -3 4 HD1 CD1 CG CB -3 4 HD2 CD2 CG CB -LYS 7 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD CE CG -2 6 HE CE NZ CD -2 4 HZ NZ CE CD -LYSH 7 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD CE CG -2 6 HE CE NZ CD -3 4 HZ NZ CE CD -MET 5 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG SD CB -3 4 HE CE SD CG -NAC 2 -1 1 H N -C CA -3 4 HA CA N -C -NH2 1 -2 3 H N -C -CA -PHE 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD1 CD1 CG CE1 -1 1 HD2 CD2 CG CE2 -1 1 HE1 CE1 CD1 CZ -1 1 HE2 CE2 CD2 CZ -1 1 HZ CZ CE1 CE2 -PRO 4 -1 5 HA CA N C CB -2 6 HB CB CG CA -2 6 HG CG CD CB -2 6 HD CD N CG -SER 4 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB OG CA -1 2 HG OG CB CA -THR 5 -1 1 H N -C CA -1 5 HA CA N C CB -1 5 HB CB CA OG1 CG2 -1 2 HG1 OG1 CB CA -3 4 HG2 CG2 CB CA -TRP 9 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD1 CD1 NE1 CG -1 1 HE1 NE1 CD1 CE2 -1 1 HE3 CE3 CD2 CZ3 -1 1 HZ3 CZ3 CE3 CH2 -1 1 HH2 CH2 CZ3 CZ2 -1 1 HZ2 CZ2 CE2 CH2 -TYR 8 -1 1 H N -C CA -1 5 HA CA N C CB -2 6 HB CB CG CA -1 1 HD1 CD1 CG CE1 -1 1 HD2 CD2 CG CE2 -1 1 HE1 CE1 CD1 CZ -1 1 HE2 CE2 CD2 CZ -1 2 HH OH CZ CE1 -VAL 5 -1 1 H N -C CA -1 5 HA CA N C CB -1 5 HB CB CA CG1 CG2 -3 4 HG1 CG1 CB CA -3 4 HG2 CG2 CB CA diff --git a/share/top/encadv.ff/aminoacids.n.tdb b/share/top/encadv.ff/aminoacids.n.tdb deleted file mode 100644 index fca14db284..0000000000 --- a/share/top/encadv.ff/aminoacids.n.tdb +++ /dev/null @@ -1,49 +0,0 @@ -[ None ] - -[ NH3+ ] -[ replace ] -N M3 14.0067 -0.91 -[ add ] -3 4 H N CA C - HN 1.008 0.37 -[ delete ] -H -[ dihedrals ] -H1 N CA C -[ impropers ] -H1 CA N H2 improper_X_X_M3_X -H1 CA N H3 improper_X_X_M3_X - -[ NH2 ] -[ replace ] -N N2 14.0067 -0.666 -[ add ] -2 4 H N CA C - HN 1.008 0.333 -[ delete ] -H -[ dihedrals ] -H1 N CA C -[ impropers ] -H1 CA N H2 improper_X_X_M_X - -[ PRO-NH2+ ] -[ replace ] -N N2 14.0067 -0.666 -[ add ] -2 4 H N CA C - HN 1.008 0.333 -[ dihedrals ] -H1 N CA C -[ impropers ] -H1 CA N H2 improper_X_X_M_X - -[ PRO-NH ] -[ replace ] -N N1 14.0067 -0.333 -[ add ] -1 4 H N CA C - HN 1.008 0.333 -[ dihedrals ] -H1 N CA C - diff --git a/share/top/encadv.ff/aminoacids.r2b b/share/top/encadv.ff/aminoacids.r2b deleted file mode 100644 index 823db9041c..0000000000 --- a/share/top/encadv.ff/aminoacids.r2b +++ /dev/null @@ -1,7 +0,0 @@ -; rtp residue to rtp building block table -;GMX Force-field -CYS CYSH -HISD HISA -HISE HISB -LYS LYSH -LYSN LYS diff --git a/share/top/encadv.ff/aminoacids.rtp b/share/top/encadv.ff/aminoacids.rtp deleted file mode 100644 index 7682e6a9a5..0000000000 --- a/share/top/encadv.ff/aminoacids.rtp +++ /dev/null @@ -1,1983 +0,0 @@ -; -; Encad residue topology file. -; Note that this is only a subset of all molecules described -; in Encad. If you need to use a new one, it might help to -; study the parameter files of Encad. -; -[ bondedtypes ] -; Column 1 : default bondtype -; Column 2 : default angletype -; Column 3 : default proper dihedraltype -; Column 4 : default improper dihedraltype -; Column 5 : This controls the generation of dihedrals from the bonding. -; All possible dihedrals are generated automatically. A value of -; 1 here means that all these are retained. A value of -; 0 here requires generated dihedrals be removed if -; * there are any dihedrals on the same central atoms -; specified in the residue topology, or -; * there are other identical generated dihedrals -; sharing the same central atoms, or -; * there are other generated dihedrals sharing the -; same central bond that have fewer hydrogen atoms -; Column 6 : number of neighbors to exclude from non-bonded interactions -; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms -; 0 = do not generate such -; Column 8 : 1 = remove proper dihedrals if found centered on the same -; bond as an improper dihedral -; 0 = do not generate such -; bonds angles dihedrals impropers all_dihedrals nrexcl bHH14 bRemoveDih - 1 1 1 1 0 3 1 - - -[ ACE ] - [ atoms ] - CH3 C3 -0.357 1 - HH31 H 0.119 1 - HH32 H 0.119 1 - HH33 H 0.119 1 - C Aprime 0.380 2 - O O -0.380 2 - [ bonds ] - CH3 HH31 - CH3 HH32 - CH3 HH33 - CH3 C - C O -[ dihedrals ] - HH33 CH3 C +N - CH3 C +N +CA -[ impropers ] - C HH33 CH3 HH31 improper_X_X_C_X - C HH33 CH3 HH32 improper_X_X_C_X - CH3 +N C O improper_X_X_A_X - - -[ ALA ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C3 -0.357 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - HB3 H 0.119 2 - C Aprime 0.380 3 - O O -0.380 3 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB HB3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB HB3 - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA HB3 CB HB1 improper_X_X_C_X - CA HB3 CB HB2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ ARG ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - NE M1 -0.333 5 - HE HN 0.333 5 - CZ A6 0.000 6 - NH1 M2 -0.666 7 - HH11 HN 0.383 7 - HH12 HN 0.383 7 - NH2 M2 -0.666 8 - HH21 HN 0.383 8 - HH22 HN 0.383 8 - C Aprime 0.380 9 - O O -0.380 9 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD NE - NE HE - NE CZ - CZ NH1 - CZ NH2 - NH1 HH11 - NH1 HH12 - NH2 HH21 - NH2 HH22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD NE - CG CD NE CZ - CD NE CZ NH2 - NE CZ NH1 HH12 - NE CZ NH2 HH22 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG NE CD HD1 improper_X_X_C_X - CG NE CD HD2 improper_X_X_C_X - CD CZ NE HE improper_X_X_M_X - NE NH2 CZ NH1 improper_X_X_A_X - CZ HH12 NH1 HH11 improper_X_X_M_X - CZ HH22 NH2 HH21 improper_X_X_M_X - - -[ ARGN ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - NE M1 -0.333 5 - HE HN 0.383 5 - CZ A6 0.000 6 - NH1 M1 -0.333 7 - HH1 HN 0.333 7 - NH2 M2 -0.666 8 - HH21 HN 0.333 8 - HH22 HN 0.333 8 - C Aprime 0.380 9 - O O -0.380 9 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD NE - NE HE - NE CZ - CZ NH1 - CZ NH2 - NH1 HH1 - NH2 HH21 - NH2 HH22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD NE - CG CD NE CZ - CD NE CZ NH2 - NE CZ NH1 HH1 - NE CZ NH2 HH22 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG NE CD HD1 improper_X_X_C_X - CG NE CD HD2 improper_X_X_C_X - CD CZ NE HE improper_X_X_M_X - NE NH1 CZ NH2 improper_X_X_A_X - CZ HH21 NH2 HH22 improper_X_X_M_X - - -[ ASN ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG Aprime 0.380 3 - OD1 O -0.380 3 - ND2 N2 -0.666 4 - HD21 HN 0.333 4 - HD22 HN 0.333 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG OD1 - CG ND2 - ND2 HD21 - ND2 HD22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG ND2 - CB CG ND2 HD22 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB ND2 CG OD1 improper_X_X_A_X - CG HD22 ND2 HD21 improper_X_X_N_X - - -[ ASP ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG Abis 0.640 3 - OD1 Obis -0.420 3 - OD2 Obis -0.420 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG OD1 - CG OD2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG OD2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB OD2 CG OD1 improper_X_X_A_X - - -[ ASPH ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG Aprime 0.380 3 - OD1 O -0.380 3 - OD2 OH -0.433 4 - HD2 HO 0.433 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG OD1 - CG OD2 - OD2 HD2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG OD2 - CB CG OD2 HD2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - OD2 CB CG OD1 improper_X_X_A_X - - - -[ CYS2 ] ; aka CYX - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - SG S 0.000 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB SG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB SG - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA SG CB HB1 improper_X_X_C_X - CA SG CB HB2 improper_X_X_C_X - - -[ CYSH ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - SG SH -0.200 3 - HG H 0.200 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB SG - SG HG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB SG - CA CB SG HG - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA SG CB HB1 improper_X_X_C_X - CA SG CB HB2 improper_X_X_C_X - - -[ CYH ] ; same as cysh - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - SG SH -0.200 3 - HG H 0.200 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB SG - SG HG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB SG - CA CB SG HG - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA SG CB HB1 improper_X_X_C_X - CA SG CB HB2 improper_X_X_C_X - - - -[ GLN ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD Aprime 0.380 4 - OE1 O -0.380 4 - NE2 N2 -0.666 5 - HE21 HN 0.333 5 - HE22 HN 0.333 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD OE1 - CD NE2 - NE2 HE21 - NE2 HE22 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - CA CB CG CD - CB CG CD NE2 - CG CD NE2 HE22 - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA +N C O improper_X_X_A_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG NE2 CD OE1 improper_X_X_A_X - CD HE22 NE2 HE21 improper_X_X_N_X - - -[ GLU ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD Abis 0.640 4 - OE1 Obis -0.420 4 - OE2 Obis -0.420 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD OE1 - CD OE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD OE2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG OE2 CD OE1 improper_X_X_A_X - - -[ GLUH ] - [ atoms ] - N N1 -0.333 1 - H HN 0.333 1 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD Aprime 0.380 4 - OE1 O -0.380 4 - OE2 OH -0.433 5 - HE2 HO 0.433 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD OE1 - CD OE2 - OE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD OE2 - CG CD OE2 HE2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG OE2 CD OE1 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ GLY ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C2 -0.238 1 - HA1 H 0.119 1 - HA2 H 0.119 1 - C Aprime 0.380 2 - O O -0.380 2 - [ bonds ] - N H - N CA - CA HA1 - CA HA2 - CA C - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA C +N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA1 improper_X_X_C_X - N C CA HA2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ HISA ] ; A.K.A. HISD/HID - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.333 4 - HD1 HN 0.333 4 - CE1 A5 0.081 5 - HE1 H 0.119 5 - NE2 L5 -0.400 5 - CD2 A5 0.081 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HID ] ; same as HISA - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.333 4 - HD1 HN 0.333 4 - CE1 A5 0.081 5 - HE1 H 0.119 5 - NE2 L5 -0.400 5 - CD2 A5 0.081 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HIS1 ] Identical to HISA - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.333 4 - HD1 HN 0.333 4 - CE1 A5 0.081 5 - HE1 H 0.119 5 - NE2 L5 -0.400 5 - CD2 A5 0.081 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ HISB ] ; A.K.A. HISE/HIE - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.200 3 - ND1 L5 -0.400 3 - CE1 A5 0.081 3 - HE1 H 0.119 3 - NE2 N1 -0.333 4 - HE2 HN 0.333 4 - CD2 A5 -0.119 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - NE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - CE1 CD2 NE2 HE2 improper_X_X_N_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ HIE ] ; same as HISB - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.200 3 - ND1 L5 -0.400 3 - CE1 A5 0.081 3 - HE1 H 0.119 3 - NE2 N1 -0.333 4 - HE2 HN 0.333 4 - CD2 A5 -0.119 5 - HD2 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - NE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - CE1 CD2 NE2 HE2 improper_X_X_N_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HISH ] ; also known as HISP (or HIS+) - [ atoms ] - N N1 -0.333 1 - H HN 0.333 1 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.300 4 - HD1 HN 0.375 4 - CE1 A5 -0.119 6 - HE1 H 0.119 6 - NE2 N1 -0.300 7 - HE2 HN 0.375 7 - CD2 A5 -0.119 5 - HD2 H 0.119 5 - C Aprime 0.380 8 - O O -0.380 8 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - NE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - CE1 CD2 NE2 HE2 improper_X_X_N_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ HIP ] ; same as HISH - [ atoms ] - N N1 -0.333 1 - H HN 0.333 1 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - ND1 N1 -0.300 4 - HD1 HN 0.375 4 - CE1 A5 -0.119 6 - HE1 H 0.119 6 - NE2 N1 -0.300 7 - HE2 HN 0.375 7 - CD2 A5 -0.119 5 - HD2 H 0.119 5 - C Aprime 0.380 8 - O O -0.380 8 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG ND1 - CG CD2 - ND1 HD1 - ND1 CE1 - CD2 HD2 - CD2 NE2 - CE1 HE1 - CE1 NE2 - NE2 HE2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG ND1 CE1 - CG ND1 CE1 NE2 - ND1 CE1 NE2 CD2 - CE1 NE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG ND1 improper_X_X_A_X - CG CE1 ND1 HD1 improper_X_X_N_X - ND1 NE2 CE1 HE1 improper_X_X_A_X - CE1 CD2 NE2 HE2 improper_X_X_N_X - NE2 CG CD2 HD2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - -[ HOH ] -; SPC and encad water have identical charges. -; Include encadwater.itp instead of spc.itp to use the flexible encad bonds/angles -; instead of the rigid SPC model. - [ atoms ] - OW OW -0.82 0 - HW1 HW 0.41 0 - HW2 HW 0.41 0 - [ bonds ] - OW HW1 - OW HW2 - - -[ ILE ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C1 -0.119 2 - HB H 0.119 2 - CG2 C3 -0.357 3 - HG21 H 0.119 3 - HG22 H 0.119 3 - HG23 H 0.119 3 - CG1 C2 -0.238 4 - HG11 H 0.119 4 - HG12 H 0.119 4 - CD C3 -0.357 5 - HD1 H 0.119 5 - HD2 H 0.119 5 - HD3 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB - CB CG1 - CB CG2 - CG1 HG11 - CG1 HG12 - CG1 CD - CG2 HG21 - CG2 HG22 - CG2 HG23 - CD HD1 - CD HD2 - CD HD3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG1 - N CA C +N - CA CB CG2 HG23 - CA CB CG1 CD - CB CG1 CD HD3 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG1 CB CG2 improper_C1_C2_C1_C3 - CA CG1 CB HB improper_X_X_C_X - CB CD CG1 HG11 improper_X_X_C_X - CB CD CG1 HG12 improper_X_X_C_X - CG1 HD3 CD HD1 improper_X_X_C_X - CG1 HD3 CD HD2 improper_X_X_C_X - CB HG23 CG2 HG21 improper_X_X_C_X - CB HG23 CG2 HG22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ LEU ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C1 -0.119 3 - HG H 0.119 3 - CD1 C3 -0.357 4 - HD11 H 0.119 4 - HD12 H 0.119 4 - HD13 H 0.119 4 - CD2 C3 -0.357 5 - HD21 H 0.119 5 - HD22 H 0.119 5 - HD23 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG - CG CD1 - CG CD2 - CD1 HD11 - CD1 HD12 - CD1 HD13 - CD2 HD21 - CD2 HD22 - CD2 HD23 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 HD13 - CB CG CD2 HD23 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG HG improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_C_X - CG HD13 CD1 HD11 improper_X_X_C_X - CG HD13 CD1 HD12 improper_X_X_C_X - CG HD23 CD2 HD21 improper_X_X_C_X - CG HD23 CD2 HD22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ LYS ] ; non-protonated - see LYSH for the most common state. - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - CE C2 -0.238 5 - HE1 H 0.119 5 - HE2 H 0.119 5 - NZ N2 -0.666 6 - HZ1 HN 0.333 6 - HZ2 HN 0.333 6 - C Aprime 0.380 7 - O O -0.380 7 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD CE - CE HE1 - CE HE2 - CE NZ - NZ HZ1 - NZ HZ2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD CE - CG CD CE NZ - CD CE NZ HZ2 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG CE CD HD1 improper_X_X_C_X - CG CE CD HD2 improper_X_X_C_X - CD NZ CE HE1 improper_X_X_C_X - CD NZ CE HE2 improper_X_X_C_X - CE HZ2 NZ HZ1 improper_X_X_M_X - CA +N C O improper_X_X_A_X - - - -[ LYSH ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD C2 -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - CE C2 -0.238 5 - HE1 H 0.119 5 - HE2 H 0.119 5 - NZ M3 -0.910 6 - HZ1 HN 0.370 6 - HZ2 HN 0.370 6 - HZ3 HN 0.370 6 - C Aprime 0.380 7 - O O -0.380 7 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD CE - CE HE1 - CE HE2 - CE NZ - NZ HZ1 - NZ HZ2 - NZ HZ3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD CE - CG CD CE NZ - CD CE NZ HZ3 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG CE CD HD1 improper_X_X_C_X - CG CE CD HD2 improper_X_X_C_X - CD NZ CE HE1 improper_X_X_C_X - CD NZ CE HE2 improper_X_X_C_X - CE HZ3 NZ HZ1 improper_X_X_M3_X - CE HZ3 NZ HZ2 improper_X_X_M3_X - CA +N C O improper_X_X_A_X - - -[ MET ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG C2 -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - SD S 0.000 4 - CE C3 -0.357 5 - HE1 H 0.119 5 - HE2 H 0.119 5 - HE3 H 0.119 5 - C Aprime 0.380 6 - O O -0.380 6 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG SD - SD CE - CE HE1 - CE HE2 - CE HE3 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG SD - CB CG SD CE - CG SD CE HE3 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB SD CG HG1 improper_X_X_C_X - CB SD CG HG2 improper_X_X_C_X - SD HE3 CE HE1 improper_X_X_C_X - SD HE3 CE HE2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ NAC ] ; metylamide, a.k.a NMA. - [ atoms ] - N N1 -0.333 1 - H HN 0.333 1 - CH3 C3 -0.357 2 - HH31 H 0.119 2 - HH32 H 0.119 2 - HH33 H 0.119 2 - [ bonds ] - N H - N CH3 - CH3 HH31 - CH3 HH32 - CH3 HH33 - -C N - [ dihedrals ] - -CA -C N CH3 - -C N CH3 HH33 - [ impropers ] - -C CH3 N H improper_X_X_N_X - N HH33 CH3 HH31 improper_X_X_C_X - N HH33 CH3 HH32 improper_X_X_C_X - - -[ NH2 ] - [ atoms ] - N N2 -0.666 1 - H1 HN 0.333 1 - H2 HN 0.333 1 - [ bonds ] - -C N - N H1 - N H2 - [ dihedrals ] - -CA -C N H2 - [ impropers ] - -C H2 N H1 improper_X_X_N_X - - -[ NHE ] -; same as NH2 - [ atoms ] - N N2 -0.666 1 - H1 HN 0.333 1 - H2 HN 0.333 1 - [ bonds ] - -C N - N H1 - N H2 - [ dihedrals ] - -CA -C N H2 - [ impropers ] - -C H2 N H1 improper_X_X_N_X - - -[ PHE ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A6 0.000 3 - CD1 A6 -0.119 4 - HD1 H 0.119 4 - CE1 A6 -0.119 5 - HE1 H 0.119 5 - CZ A6 -0.119 6 - HZ H 0.119 6 - CE2 A6 -0.119 7 - HE2 H 0.119 7 - CD2 A6 -0.119 8 - HD2 H 0.119 8 - C Aprime 0.380 9 - O O -0.380 9 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG CD1 - CG CD2 - CD1 HD1 - CD1 CE1 - CD2 HD2 - CD2 CE2 - CE1 HE1 - CE1 CZ - CE2 HE2 - CE2 CZ - CZ HZ - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 CE1 - CB CG CD2 CE2 - CG CD1 CE1 CZ - CD1 CE1 CZ CE2 - CE1 CZ CE2 CD2 - CZ CE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_A_X - CG CE1 CD1 HD1 improper_X_X_A_X - CD1 CZ CE1 HE1 improper_X_X_A_X - CE1 CE2 CZ HZ improper_X_X_A_X - CE2 CG CD2 HD2 improper_X_X_A_X - CZ CD2 CE2 HE2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - -[ PRO ] - [ atoms ] - N N 0.000 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB CP -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG CP -0.238 3 - HG1 H 0.119 3 - HG2 H 0.119 3 - CD CP -0.238 4 - HD1 H 0.119 4 - HD2 H 0.119 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG HG1 - CG HG2 - CG CD - CD HD1 - CD HD2 - CD N - C O - -C N - [ dihedrals ] - -CA -C N CD - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD - CB CG CD N - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD CG HG1 improper_X_X_C_X - CB CD CG HG2 improper_X_X_C_X - CG N CD HD1 improper_X_X_C_X - CG N CD HD2 improper_X_X_C_X - -C CD N CA improper_X_X_N_X - CA +N C O improper_X_X_A_X - - - -[ SER ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - OG OH -0.433 3 - HG HO 0.433 3 - C Aprime 0.380 4 - O O -0.380 4 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB OG - OG HG - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB OG - N CA C +N - CA CB OG HG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA OG CB HB1 improper_X_X_C_X - CA OG CB HB2 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ THR ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C1 -0.119 2 - HB H 0.119 2 - OG1 OH -0.433 3 - HG1 HO 0.433 3 - CG2 C3 -0.357 4 - HG21 H 0.119 4 - HG22 H 0.119 4 - HG23 H 0.119 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB - CB OG1 - CB CG2 - OG1 HG1 - CG2 HG21 - CG2 HG22 - CG2 HG23 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG2 - N CA C +N - CA CB OG1 HG1 - CA CB CG2 HG23 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG2 CB OG1 improper_X_X_C_X - CA CG2 CB HB improper_X_X_C_X - CB HG23 CG2 HG21 improper_X_X_C_X - CB HG23 CG2 HG22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - -[ TRP ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A5 0.000 3 - CD1 A5 -0.119 4 - HD1 H 0.119 4 - NE1 N1 -0.333 5 - HE1 HN 0.333 5 - CE2 A7 0.000 6 - CZ2 A6 -0.119 7 - HZ2 H 0.119 7 - CH2 A6 -0.119 8 - HH2 H 0.119 8 - CZ3 A6 -0.119 9 - HZ3 H 0.119 9 - CE3 A6 -0.119 10 - HE3 H 0.119 10 - CD2 A7 0.000 11 - C Aprime 0.380 12 - O O -0.380 12 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG CD1 - CG CD2 - CD1 HD1 - CD1 NE1 - CD2 CE2 - CD2 CE3 - NE1 HE1 - NE1 CE2 - CE2 CZ2 - CE3 HE3 - CE3 CZ3 - CZ2 HZ2 - CZ2 CH2 - CZ3 HZ3 - CZ3 CH2 - CH2 HH2 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 NE1 - CG CD1 NE1 CE2 - CD1 NE1 CE2 CD2 - NE1 CE2 CD2 CE3 - NE1 CE2 CZ2 CH2 - CE2 CZ2 CH2 CZ3 - CZ2 CH2 CZ3 CE3 - CH2 CZ3 CE3 CD2 - CZ3 CE3 CD2 CE2 - CB CG CD2 CE3 - [ impropers ] - -C CA N H improper_X_X_N_X - CA +N C O improper_X_X_A_X - N C CA CB improper_N_A_C1_C - N C CA HA improper_X_X_C_X - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_A_X - CG NE1 CD1 HD1 improper_X_X_A_X - CD1 CE2 NE1 HE1 improper_X_X_N_X - NE1 CD2 CE2 CZ2 improper_X_X_A_X - CE2 CH2 CZ2 HZ2 improper_X_X_A_X - CZ2 CZ3 CH2 HH2 improper_X_X_A_X - CH2 CE3 CZ3 HZ3 improper_X_X_A_X - CZ3 CD2 CE3 HE3 improper_X_X_A_X - CG CD2 CE2 CE3 improper_X_X_A_X - - -[ TYR ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C2 -0.238 2 - HB1 H 0.119 2 - HB2 H 0.119 2 - CG A6 0.000 3 - CD1 A6 -0.119 4 - HD1 H 0.119 4 - CE1 A6 -0.119 5 - HE1 H 0.119 5 - CZ A6 0.000 6 - OH OH -0.433 7 - HH HO 0.433 7 - CE2 A6 -0.119 8 - HE2 H 0.119 8 - CD2 A6 -0.119 9 - HD2 H 0.119 9 - C Aprime 0.380 10 - O O -0.380 10 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB1 - CB HB2 - CB CG - CG CD1 - CG CD2 - CD1 HD1 - CD1 CE1 - CD2 HD2 - CD2 CE2 - CE1 HE1 - CE1 CZ - CE2 HE2 - CE2 CZ - CZ OH - OH HH - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG - N CA C +N - CA CB CG CD2 - CB CG CD1 CE1 - CB CG CD2 CE2 - CG CD1 CE1 CZ - CD1 CE1 CZ CE2 - CE1 CZ OH HO - CE1 CZ CE2 CD2 - CZ CE2 CD2 CG - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG CB HB1 improper_X_X_C_X - CA CG CB HB2 improper_X_X_C_X - CB CD2 CG CD1 improper_X_X_A_X - CG CE1 CD1 HD1 improper_X_X_A_X - CD1 CZ CE1 HE1 improper_X_X_A_X - CE1 CE2 CZ OH improper_X_X_A_X - CE2 CG CD2 HD2 improper_X_X_A_X - CZ CD2 CE2 HE2 improper_X_X_A_X - CA +N C O improper_X_X_A_X - - - - -[ VAL ] - [ atoms ] - N N1 -0.333 0 - H HN 0.333 0 - CA C1 -0.119 1 - HA H 0.119 1 - CB C1 -0.119 2 - HB H 0.119 2 - CG1 C3 -0.357 3 - HG11 H 0.119 3 - HG12 H 0.119 3 - HG13 H 0.119 3 - CG2 C3 -0.357 4 - HG21 H 0.119 4 - HG22 H 0.119 4 - HG23 H 0.119 4 - C Aprime 0.380 5 - O O -0.380 5 - [ bonds ] - N H - N CA - CA HA - CA CB - CA C - CB HB - CB CG1 - CB CG2 - CG1 HG11 - CG1 HG12 - CG1 HG13 - CG2 HG21 - CG2 HG22 - CG2 HG23 - C O - -C N - [ dihedrals ] - -CA -C N CA - -C N CA C - N CA CB CG2 - N CA C +N - CA CB CG2 HG23 - CA CB CG1 HG13 - [ impropers ] - -C CA N H improper_X_X_N_X - N C CA HA improper_X_X_C_X - N C CA CB improper_N_A_C1_C - CA CG2 CB HB improper_X_X_C_X - CA CG2 CB CG1 improper_X_X_C_X - CB HG13 CG1 HG11 improper_X_X_C_X - CB HG13 CG1 HG12 improper_X_X_C_X - CB HG23 CG2 HG21 improper_X_X_C_X - CB HG23 CG2 HG22 improper_X_X_C_X - CA +N C O improper_X_X_A_X - - - -[ CL ] - [ atoms ] - CL CL -1.000 0 - -[ NA ] - [ atoms ] - NA NA 1.000 0 - -[ FE ] - [ atoms ] - FE FE 2.000 0 - -[ Ar ] - [ atoms ] - AR AR 0.000 0 - diff --git a/share/top/encadv.ff/atomtypes.atp b/share/top/encadv.ff/atomtypes.atp deleted file mode 100644 index 719113ed1f..0000000000 --- a/share/top/encadv.ff/atomtypes.atp +++ /dev/null @@ -1,43 +0,0 @@ - H 1.008 ; Hydrogen bound to carbon - O 15.9994 ; Oxygen - N 14.0067 ; Trivalent nitrogen - N1 14.0067 ; Trivalent nitrogen - N2 14.0067 ; Trivalent nitrogen - C1 12.011 ; Aliphatic carbon - C2 12.011 ; Aliphatic carbon - C3 12.011 ; Aliphatic carbon - CP 12.011 ; Aliphatic carbon - A6 12.011 ; Aromatic carbon - A5 12.011 ; Aromatic carbon - A7 12.011 ; Aromatic carbon - Aprime 12.011 ; Aromatic carbon - Abis 12.011 ; Aromatic carbon - L5 14.0067 ; Acceptor nitrogen - L6 14.0067 ; Acceptor nitrogen - P 30.9738 ; Phosphorus - OH 15.9994 ; Divalent oxygen - O2 15.9994 ; Divalent oxygen - OR 15.9994 ; Divalent oxygen - S 32.060 ; Sulphur not bound to hydrogen - SH 32.060 ; Sulphur with bound hydrogen - M1 14.0067 ; Charged nitrogen - M2 14.0067 ; Charged nitrogen - M3 14.0067 ; Charged nitrogen - HN 1.008 ; Polar hydrogen - HO 1.008 ; Polar hydrogen - HW 1.008 ; Water hydrogen - CL 35.453 ; Chloride ion - Obis 15.9994 ; Charged oxygen - OP 15.9994 ; Charged oxygen - R 14.0067 ; Heme nitrogen - W 14.0067 ; Heme nitrogen - Y 12.011 ; Heme carbon - Z 12.011 ; Heme carbon - FE 55.847 ; Heme Iron - OF 15.9994 ; Heme oxygen - OW 15.9994 ; Water oxygen - AR 39.948 ; Argon - NA 22.9898 ; Sodium - MCH3 0 ; Dummy - MNH3 0 ; Dummy - MW 0 ; Dummy diff --git a/share/top/encadv.ff/ffbonded.itp b/share/top/encadv.ff/ffbonded.itp deleted file mode 100644 index 2adf6eabdc..0000000000 --- a/share/top/encadv.ff/ffbonded.itp +++ /dev/null @@ -1,856 +0,0 @@ -[ bondtypes ] - ; i j func b0 kb - OW HW 1 0.10000 209200.0 - OH HO 1 0.10000 209200.0 - N1 HN 1 0.10000 209200.0 - N2 HN 1 0.10000 209200.0 - C1 H 1 0.10900 209200.0 - C2 H 1 0.10900 209200.0 - C3 H 1 0.10900 209200.0 - CP H 1 0.10900 209200.0 - C1 O 1 0.14370 209200.0 - C2 O2 1 0.14370 209200.0 - C2 OR 1 0.14370 209200.0 - C1 OH 1 0.14390 209200.0 - C2 OH 1 0.14390 209200.0 - C3 OH 1 0.14390 209200.0 - C1 N 1 0.14670 209200.0 - C1 N1 1 0.14670 209200.0 - C1 N2 1 0.14670 209200.0 - C2 N 1 0.14670 209200.0 - C2 N1 1 0.14670 209200.0 - C2 N2 1 0.14670 209200.0 - C3 N 1 0.14670 209200.0 - C3 N1 1 0.14670 209200.0 - C3 N2 1 0.14670 209200.0 - CP N 1 0.14670 209200.0 - CP N1 1 0.14670 209200.0 - CP N2 1 0.14670 209200.0 - C1 M1 1 0.14720 209200.0 - C1 M2 1 0.14720 209200.0 - C1 M3 1 0.14720 209200.0 - C2 M1 1 0.14720 209200.0 - C2 M2 1 0.14720 209200.0 - C2 M3 1 0.14720 209200.0 - C3 M1 1 0.14720 209200.0 - C3 M2 1 0.14720 209200.0 - C3 M3 1 0.14720 209200.0 - C1 C1 1 0.15250 209200.0 - C1 C2 1 0.15250 209200.0 - C1 C3 1 0.15250 209200.0 - C2 C2 1 0.15250 209200.0 - C2 C3 1 0.15250 209200.0 - C3 C3 1 0.15250 209200.0 - CP CP 1 0.15190 209200.0 - C1 CP 1 0.14980 209200.0 - A6 H 1 0.10900 209200.0 - A5 H 1 0.10900 209200.0 - A7 H 1 0.10900 209200.0 - A6 C1 1 0.15260 209200.0 - A6 C2 1 0.15260 209200.0 - A6 C3 1 0.15260 209200.0 - A6 OH 1 0.13780 209200.0 - A7 C1 1 0.15260 209200.0 - A7 C2 1 0.15260 209200.0 - A7 C3 1 0.15260 209200.0 - Aprime C1 1 0.15260 209200.0 - Abis C1 1 0.15260 209200.0 - Aprime C2 1 0.15260 209200.0 - Aprime C3 1 0.15260 209200.0 - Abis C2 1 0.15260 209200.0 - Abis C3 1 0.15260 209200.0 - Aprime O 1 0.12360 418400.0 - Aprime OH 1 0.12360 418400.0 - Abis Obis 1 0.12230 418400.0 - Aprime N 1 0.13220 418400.0 - Aprime N1 1 0.13220 418400.0 - Aprime N2 1 0.13220 418400.0 - A5 N 1 0.13340 418400.0 - A5 N1 1 0.13340 418400.0 - A5 N2 1 0.13340 418400.0 - A5 C1 1 0.15160 209200.0 - A5 C2 1 0.15160 209200.0 - A5 C3 1 0.15160 209200.0 - A5 A5 1 0.13760 418400.0 - A5 A7 1 0.14510 418400.0 - A5 L5 1 0.13340 418400.0 - A6 O 1 0.12280 418400.0 - A6 O2 1 0.12280 418400.0 - A6 OR 1 0.12280 418400.0 - A6 A6 1 0.13890 418400.0 - A6 A7 1 0.14110 418400.0 - A6 M1 1 0.13350 418400.0 - A6 M2 1 0.13350 418400.0 - A6 M3 1 0.13350 418400.0 - A7 N 1 0.13670 418400.0 - A7 N2 1 0.13670 418400.0 - A7 N1 1 0.13430 418400.0 - A7 A7 1 0.13640 418400.0 - SH H 1 0.13300 209200.0 - S C2 1 0.18080 209200.0 - S C3 1 0.18080 209200.0 - SH C2 1 0.18080 209200.0 - S S 1 0.20150 209200.0 - M1 HN 1 0.10000 209200.0 - M2 HN 1 0.10000 209200.0 - M3 HN 1 0.10000 209200.0 - A6 N 1 0.13550 418400.0 - A6 N1 1 0.13550 418400.0 - A6 N2 1 0.13550 418400.0 - A6 L5 1 0.13550 418400.0 - A6 L6 1 0.13550 418400.0 - A7 L5 1 0.13670 418400.0 - A7 L6 1 0.13670 418400.0 - P OP 1 0.14800 418400.0 - P O2 1 0.15940 209200.0 - Y A6 1 0.13960 418400.0 - Y Aprime 1 0.13960 418400.0 - Y R 1 0.13840 418400.0 - Y W 1 0.13840 418400.0 - Z C2 1 0.15170 209200.0 - Z C3 1 0.15170 209200.0 - Z A6 1 0.14900 418400.0 - Z Aprime 1 0.14900 418400.0 - Z Y 1 0.14440 418400.0 - Z Z 1 0.13570 418400.0 - FE N 1 0.19800 58576.0 - FE N1 1 0.19800 58576.0 - FE N2 1 0.19800 58576.0 - FE W 1 0.19800 58576.0 - OF FE 1 0.16320 58576.0 ; iron-oxygen bond - OF OF 1 0.12240 418400.0 - -;[ constrainttypes ] - -[ angletypes ] - ; i j k func th0 cth - HW OW HW 1 109.47 502.08 - C1 OH HO 1 110.00 502.08 - C2 OH HO 1 110.00 502.08 - C3 OH HO 1 110.00 502.08 - Aprime OH HO 1 110.00 502.08 - A6 OH HO 1 110.00 502.08 - C1 C1 Abis 1 110.10 502.08 - C2 C1 Abis 1 110.10 502.08 - C3 C1 Abis 1 110.10 502.08 - HN N2 HN 1 120.00 502.08 - CP N1 HN 1 119.50 502.08 - CP N2 HN 1 119.50 502.08 - C1 N1 HN 1 119.50 502.08 - C1 N2 HN 1 119.50 502.08 - C2 N1 HN 1 119.50 502.08 - C2 N2 HN 1 119.50 502.08 - C3 N1 HN 1 119.50 502.08 - C3 N2 HN 1 119.50 502.08 - A6 N1 HN 1 119.60 502.08 - A6 N2 HN 1 119.60 502.08 - A5 N1 HN 1 119.60 502.08 - A5 N2 HN 1 119.60 502.08 - A7 N1 HN 1 119.60 502.08 - A7 N2 HN 1 119.60 502.08 - Aprime N1 HN 1 119.60 502.08 - Aprime N2 HN 1 119.60 502.08 - N2 Aprime N2 1 113.00 502.08 - C2 Aprime C3 1 118.00 502.08 - C1 N C1 1 112.40 502.08 - C1 N C2 1 112.40 502.08 - C1 N C3 1 112.40 502.08 - C1 N1 CP 1 112.40 502.08 - C1 N1 C1 1 112.40 502.08 - C1 N1 C2 1 112.40 502.08 - C1 N1 C3 1 112.40 502.08 - C1 N2 CP 1 112.40 502.08 - C1 N2 C1 1 112.40 502.08 - C1 N2 C2 1 112.40 502.08 - C1 N2 C3 1 112.40 502.08 - C2 N C2 1 112.40 502.08 - C2 N C3 1 112.40 502.08 - C2 N1 C2 1 112.40 502.08 - C2 N1 C3 1 112.40 502.08 - C2 N2 C2 1 112.40 502.08 - C2 N2 C3 1 112.40 502.08 - C3 N C3 1 112.40 502.08 - C3 N1 C3 1 112.40 502.08 - C3 N2 C3 1 112.40 502.08 - C1 N CP 1 112.40 502.08 - A6 N C1 1 121.30 502.08 - A6 N C2 1 121.30 502.08 - A6 N C3 1 121.30 502.08 - A6 N1 C1 1 121.30 502.08 - A6 N1 C2 1 121.30 502.08 - A6 N1 C3 1 121.30 502.08 - A6 N2 C1 1 121.30 502.08 - A6 N2 C2 1 121.30 502.08 - A6 N2 C3 1 121.30 502.08 - A5 N C1 1 121.30 502.08 - A5 N C2 1 121.30 502.08 - A5 N C3 1 121.30 502.08 - A5 N1 C1 1 121.30 502.08 - A5 N1 C2 1 121.30 502.08 - A5 N1 C3 1 121.30 502.08 - A5 N2 C1 1 121.30 502.08 - A5 N2 C2 1 121.30 502.08 - A5 N2 C3 1 121.30 502.08 - A7 N C1 1 121.30 502.08 - A7 N C2 1 121.30 502.08 - A7 N C3 1 121.30 502.08 - A7 N1 C1 1 121.30 502.08 - A7 N1 C2 1 121.30 502.08 - A7 N1 C3 1 121.30 502.08 - A7 N2 C1 1 121.30 502.08 - A7 N2 C2 1 121.30 502.08 - A7 N2 C3 1 121.30 502.08 - Aprime N C1 1 121.30 502.08 - Aprime N C2 1 121.30 502.08 - Aprime N C3 1 121.30 502.08 - Aprime N1 C1 1 121.30 502.08 - Aprime N1 C2 1 121.30 502.08 - Aprime N1 C3 1 121.30 502.08 - Aprime N2 C1 1 121.30 502.08 - Aprime N2 C2 1 121.30 502.08 - Aprime N2 C3 1 121.30 502.08 - A5 N A5 1 108.00 1004.16 - A5 N1 A5 1 108.00 1004.16 - A5 N2 A5 1 108.00 1004.16 - A5 N1 A7 1 108.00 1004.16 - H C1 H 1 109.50 502.08 - H C2 H 1 109.50 502.08 - H C3 H 1 109.50 502.08 - H CP H 1 109.50 502.08 - O C1 H 1 109.00 502.08 - OH C1 H 1 109.00 502.08 - OH C2 H 1 109.00 502.08 - OH C3 H 1 109.00 502.08 - O2 C2 H 1 109.00 502.08 - OR C2 H 1 109.00 502.08 - O C1 C1 1 109.50 502.08 - O C1 C2 1 109.50 502.08 - O C1 C3 1 109.50 502.08 - OH C1 C1 1 107.90 502.08 - OH C1 C2 1 107.90 502.08 - OH C1 C3 1 107.90 502.08 - OH C2 C1 1 107.90 502.08 - OH C2 C2 1 107.90 502.08 - OH C2 C3 1 107.90 502.08 - O2 C2 C1 1 109.50 502.08 - O2 C2 C2 1 109.50 502.08 - O2 C2 C3 1 109.50 502.08 - OR C2 C1 1 109.50 502.08 - OR C2 C2 1 109.50 502.08 - OR C2 C3 1 109.50 502.08 - C1 C1 H 1 109.50 502.08 - C1 C2 H 1 109.50 502.08 - C1 C3 H 1 109.50 502.08 - C1 CP H 1 109.50 502.08 - C2 C1 H 1 109.50 502.08 - C2 C2 H 1 109.50 502.08 - C2 C3 H 1 109.50 502.08 - C3 C1 H 1 109.50 502.08 - C3 C2 H 1 109.50 502.08 - C3 C3 H 1 109.50 502.08 - CP C1 H 1 109.50 502.08 - CP CP H 1 109.50 502.08 - N C1 H 1 109.50 502.08 - N C2 H 1 109.50 502.08 - N C3 H 1 109.50 502.08 - N CP H 1 109.50 502.08 - N1 CP H 1 109.50 502.08 - N1 C1 H 1 109.50 502.08 - N1 C2 H 1 109.50 502.08 - N1 C3 H 1 109.50 502.08 - N2 CP H 1 109.50 502.08 - N2 C1 H 1 109.50 502.08 - N2 C2 H 1 109.50 502.08 - N2 C3 H 1 109.50 502.08 - M1 C1 H 1 109.50 502.08 - M1 C2 H 1 109.50 502.08 - M1 C3 H 1 109.50 502.08 - M2 C1 H 1 109.50 502.08 - M2 C2 H 1 109.50 502.08 - M2 C3 H 1 109.50 502.08 - M3 C1 H 1 109.50 502.08 - M3 C2 H 1 109.50 502.08 - M3 C3 H 1 109.50 502.08 - M1 C1 C1 1 111.00 502.08 - M1 C1 C2 1 111.00 502.08 - M1 C1 C3 1 111.00 502.08 - M1 C2 C1 1 111.00 502.08 - M1 C2 C2 1 111.00 502.08 - M1 C2 C3 1 111.00 502.08 - M2 C1 C1 1 111.00 502.08 - M2 C1 C2 1 111.00 502.08 - M2 C1 C3 1 111.00 502.08 - M2 C2 C1 1 111.00 502.08 - M2 C2 C2 1 111.00 502.08 - M2 C2 C3 1 111.00 502.08 - M3 C1 C1 1 111.00 502.08 - M3 C1 C2 1 111.00 502.08 - M3 C1 C3 1 111.00 502.08 - M3 C2 C1 1 111.00 502.08 - M3 C2 C2 1 111.00 502.08 - M3 C2 C3 1 111.00 502.08 - A6 C1 H 1 109.50 502.08 - A6 C2 H 1 109.50 502.08 - A6 C3 H 1 109.50 502.08 - A5 C1 H 1 109.50 502.08 - A5 C2 H 1 109.50 502.08 - A5 C3 H 1 109.50 502.08 - A7 C1 H 1 109.50 502.08 - A7 C2 H 1 109.50 502.08 - A7 C3 H 1 109.50 502.08 - Aprime C1 H 1 109.50 502.08 - Aprime C2 H 1 109.50 502.08 - Aprime C3 H 1 109.50 502.08 - Abis C2 H 1 109.50 502.08 - Abis C3 H 1 109.50 502.08 - Abis C1 H 1 109.50 502.08 - C1 C1 N 1 109.10 502.08 - C1 C1 N1 1 109.10 502.08 - C1 C1 N2 1 109.10 502.08 - C1 C2 N 1 109.10 502.08 - C1 C2 N1 1 109.10 502.08 - C1 C2 N2 1 109.10 502.08 - C2 C1 N 1 109.10 502.08 - C2 C1 N1 1 109.10 502.08 - C2 C1 N2 1 109.10 502.08 - C2 C2 N 1 109.10 502.08 - C2 C2 N1 1 109.10 502.08 - C2 C2 N2 1 109.10 502.08 - C3 C1 N 1 109.10 502.08 - C3 C1 N1 1 109.10 502.08 - C3 C1 N2 1 109.10 502.08 - C3 C2 N 1 109.10 502.08 - C3 C2 N1 1 109.10 502.08 - C3 C2 N2 1 109.10 502.08 - CP C1 N 1 104.00 502.08 - CP C1 N1 1 109.10 502.08 - CP C1 N2 1 109.10 502.08 - A6 C1 N 1 111.30 502.08 - A6 C1 N1 1 111.30 502.08 - A6 C1 N2 1 111.30 502.08 - A6 C2 N 1 111.30 502.08 - A6 C2 N1 1 111.30 502.08 - A6 C2 N2 1 111.30 502.08 - A5 C1 N 1 111.30 502.08 - A5 C1 N1 1 111.30 502.08 - A5 C1 N2 1 111.30 502.08 - A5 C2 N 1 111.30 502.08 - A5 C2 N1 1 111.30 502.08 - A5 C2 N2 1 111.30 502.08 - A7 C1 N 1 111.30 502.08 - A7 C1 N1 1 111.30 502.08 - A7 C1 N2 1 111.30 502.08 - A7 C2 N 1 111.30 502.08 - A7 C2 N1 1 111.30 502.08 - A7 C2 N2 1 111.30 502.08 - Aprime C1 N 1 111.30 502.08 - Aprime C1 N1 1 111.30 502.08 - Aprime C1 N2 1 111.30 502.08 - Aprime C2 N 1 111.30 502.08 - Aprime C2 N1 1 111.30 502.08 - Aprime C2 N2 1 111.30 502.08 - Abis C2 N 1 111.30 502.08 - Abis C2 N1 1 111.30 502.08 - Abis C2 N2 1 111.30 502.08 - A6 C1 M1 1 111.30 502.08 - A6 C1 M2 1 111.30 502.08 - A6 C1 M3 1 111.30 502.08 - A6 C2 M1 1 111.30 502.08 - A6 C2 M2 1 111.30 502.08 - A6 C2 M3 1 111.30 502.08 - A5 C1 M1 1 111.30 502.08 - A5 C1 M2 1 111.30 502.08 - A5 C1 M3 1 111.30 502.08 - A5 C2 M1 1 111.30 502.08 - A5 C2 M2 1 111.30 502.08 - A5 C2 M3 1 111.30 502.08 - A7 C1 M1 1 111.30 502.08 - A7 C1 M2 1 111.30 502.08 - A7 C1 M3 1 111.30 502.08 - A7 C2 M1 1 111.30 502.08 - A7 C2 M2 1 111.30 502.08 - A7 C2 M3 1 111.30 502.08 - Aprime C1 M1 1 111.30 502.08 - Aprime C1 M2 1 111.30 502.08 - Aprime C1 M3 1 111.30 502.08 - Aprime C2 M1 1 111.30 502.08 - Aprime C2 M2 1 111.30 502.08 - Aprime C2 M3 1 111.30 502.08 - Abis C2 M1 1 111.30 502.08 - Abis C2 M2 1 111.30 502.08 - Abis C2 M3 1 111.30 502.08 - Abis C1 M1 1 111.30 502.08 - Abis C1 M2 1 111.30 502.08 - Abis C1 M3 1 111.30 502.08 - Abis C1 N 1 111.30 502.08 - Abis C1 N1 1 111.30 502.08 - Abis C1 N2 1 111.30 502.08 - C1 C1 C1 1 111.40 502.08 - C1 C1 C2 1 111.40 502.08 - C1 C1 C3 1 111.40 502.08 - C1 C2 C1 1 111.40 502.08 - C1 C2 C2 1 111.40 502.08 - C1 C2 C3 1 111.40 502.08 - C1 CP CP 1 107.20 502.08 - C2 C1 C2 1 111.40 502.08 - C2 C1 C3 1 111.40 502.08 - C2 C2 C2 1 111.40 502.08 - C2 C2 C3 1 111.40 502.08 - C3 C1 C3 1 111.40 502.08 - C3 C2 C3 1 111.40 502.08 - CP CP CP 1 103.90 502.08 - N CP CP 1 105.10 502.08 - N1 CP CP 1 105.10 502.08 - N2 CP CP 1 105.10 502.08 - Aprime N CP 1 125.80 502.08 - A6 C1 C1 1 114.10 502.08 - A6 C1 C2 1 114.10 502.08 - A6 C1 C3 1 114.10 502.08 - A6 C2 C1 1 114.10 502.08 - A6 C2 C2 1 114.10 502.08 - A6 C2 C3 1 114.10 502.08 - A5 C1 C1 1 113.90 502.08 - A5 C1 C2 1 113.90 502.08 - A5 C1 C3 1 113.90 502.08 - A5 C2 C1 1 113.90 502.08 - A5 C2 C2 1 113.90 502.08 - A5 C2 C3 1 113.90 502.08 - A7 C1 C1 1 110.10 502.08 - A7 C1 C2 1 110.10 502.08 - A7 C1 C3 1 110.10 502.08 - A7 C2 C1 1 110.10 502.08 - A7 C2 C2 1 110.10 502.08 - A7 C2 C3 1 110.10 502.08 - Aprime C1 C1 1 110.10 502.08 - Aprime C1 C2 1 110.10 502.08 - Aprime C1 C3 1 110.10 502.08 - Aprime C1 CP 1 111.90 502.08 - Abis C1 CP 1 110.10 502.08 - Aprime C2 C1 1 110.10 502.08 - Aprime C2 C2 1 110.10 502.08 - Aprime C2 C3 1 110.10 502.08 - Abis C2 C1 1 110.10 502.08 - Abis C2 C2 1 110.10 502.08 - Abis C2 C3 1 110.10 502.08 - S C2 C1 1 115.50 502.08 - S C2 C2 1 115.50 502.08 - S C2 C3 1 115.50 502.08 - SH C2 C1 1 115.50 502.08 - SH C2 C2 1 115.50 502.08 - SH C2 C3 1 115.50 502.08 - S C2 H 1 110.00 502.08 - S C3 H 1 110.00 502.08 - SH C2 H 1 110.00 502.08 - C2 SH H 1 110.00 502.08 - H A6 H 1 120.00 502.08 - H A5 H 1 120.00 502.08 - H A7 H 1 120.00 502.08 - A6 A6 H 1 120.00 502.08 - A6 A7 H 1 120.00 502.08 - A5 A5 H 1 126.00 502.08 - A5 A7 H 1 120.00 502.08 - A7 A6 H 1 120.00 502.08 - A7 A5 H 1 126.00 502.08 - A7 A7 H 1 120.00 502.08 - O A6 O 1 120.00 502.08 - O Aprime O 1 120.00 502.08 - OH Aprime O 1 120.00 502.08 - O2 A6 O 1 120.00 502.08 - OR A6 O 1 120.00 502.08 - N A6 H 1 120.00 502.08 - N A5 H 1 126.00 502.08 - N A7 H 1 120.00 502.08 - N1 A6 H 1 120.00 502.08 - N1 A5 H 1 126.00 502.08 - N1 A7 H 1 120.00 502.08 - N2 A6 H 1 120.00 502.08 - N2 A5 H 1 126.00 502.08 - N2 A7 H 1 120.00 502.08 - N Aprime O 1 123.50 1004.16 - N1 Aprime O 1 123.50 1004.16 - N2 Aprime O 1 123.50 1004.16 - C1 Aprime O 1 121.00 502.08 - C1 Aprime OH 1 121.00 502.08 - C2 Aprime O 1 121.00 502.08 - C2 Aprime OH 1 121.00 502.08 - C3 Aprime O 1 121.00 502.08 - C3 Aprime C3 1 121.00 502.08 - C1 Aprime N 1 115.50 502.08 - C1 Aprime N1 1 115.50 502.08 - C1 Aprime N2 1 115.50 502.08 - C2 Aprime N 1 115.50 502.08 - C2 Aprime N1 1 115.50 502.08 - C2 Aprime N2 1 115.50 502.08 - C3 Aprime N 1 115.50 502.08 - C3 Aprime N1 1 115.50 502.08 - C3 Aprime N2 1 115.50 502.08 - Obis Abis C1 1 117.70 502.08 - Obis Abis C2 1 117.70 502.08 - Obis Abis C3 1 117.70 502.08 - Obis Abis Obis 1 124.60 1004.16 - C2 A5 A5 1 126.00 502.08 - C2 A5 L5 1 126.00 502.08 - L5 A5 H 1 126.00 502.08 - C2 A5 A7 1 126.00 502.08 - A5 A5 N 1 108.00 1004.16 - A5 A5 N1 1 108.00 1004.16 - A5 A5 N2 1 108.00 1004.16 - A5 A5 L5 1 108.00 1004.16 - N1 A5 L5 1 108.00 1004.16 - C2 A5 N1 1 126.00 502.08 - A7 A5 A5 1 108.00 1004.16 - M1 A6 M1 1 120.00 1004.16 - M1 A6 M2 1 120.00 1004.16 - M1 A6 M3 1 120.00 1004.16 - M2 A6 M2 1 120.00 1004.16 - M2 A6 M3 1 120.00 1004.16 - M3 A6 M3 1 120.00 1004.16 - A6 A6 C1 1 120.10 502.08 - A6 A6 C2 1 120.10 502.08 - A6 A6 C3 1 120.10 502.08 - A6 A6 A6 1 120.00 1004.16 - A6 A6 OH 1 118.40 502.08 - A7 A6 A6 1 120.00 1004.16 - A5 A7 A7 1 108.00 1004.16 - A7 A7 A6 1 120.00 1004.16 - A5 A7 A6 1 132.00 1004.16 - N A7 A6 1 132.00 502.08 - N1 A7 A6 1 132.00 502.08 - N2 A7 A6 1 132.00 502.08 - N1 A7 A7 1 108.00 1004.16 - L5 A7 A6 1 132.00 502.08 - L6 A7 A6 1 132.00 502.08 - C2 S C2 1 99.10 502.08 - C2 S C3 1 99.10 502.08 - S S C2 1 104.30 502.08 - HN M2 HN 1 120.00 502.08 - HN M3 HN 1 109.50 502.08 - C1 M1 HN 1 119.50 502.08 - C1 M2 HN 1 119.50 502.08 - C1 M3 HN 1 109.50 502.08 - C2 M1 HN 1 119.50 502.08 - C2 M2 HN 1 119.50 502.08 - C2 M3 HN 1 109.50 502.08 - C3 M1 HN 1 119.50 502.08 - C3 M2 HN 1 119.50 502.08 - C3 M3 HN 1 109.50 502.08 - A6 M1 HN 1 119.60 502.08 - A6 M2 HN 1 119.60 502.08 - A6 M3 HN 1 119.60 502.08 - A6 M1 C1 1 123.20 502.08 - A6 M1 C2 1 123.20 502.08 - A6 M1 C3 1 123.20 502.08 - A6 M2 C1 1 123.20 502.08 - A6 M2 C2 1 123.20 502.08 - A6 M2 C3 1 123.20 502.08 - A6 M3 C1 1 123.20 502.08 - A6 M3 C2 1 123.20 502.08 - A6 M3 C3 1 123.20 502.08 - A5 L5 A5 1 108.00 1004.16 - A6 N1 A6 1 120.00 502.08 - OH C1 N 1 109.50 502.08 - OH C1 N1 1 109.50 502.08 - OH C1 N2 1 109.50 502.08 - C3 A7 A6 1 108.86 502.08 - C3 A7 A7 1 132.53 502.08 - L5 A7 A7 1 108.00 502.08 - A7 A7 L6 1 120.00 502.08 - A5 L5 A7 1 108.00 502.08 - A6 L5 A7 1 119.33 502.08 - N1 A5 N1 1 108.00 1004.16 - Y A6 H 1 120.00 502.08 - Z C2 H 1 110.00 502.08 - Z C3 H 1 110.00 502.08 - Z A6 H 1 120.00 502.08 - A6 N FE 1 120.00 502.08 - A6 N1 FE 1 120.00 502.08 - A6 N2 FE 1 120.00 502.08 - A5 N FE 1 120.00 502.08 - A5 N1 FE 1 120.00 502.08 - A5 N2 FE 1 120.00 502.08 - A7 N FE 1 120.00 502.08 - A7 N1 FE 1 120.00 502.08 - A7 N2 FE 1 120.00 502.08 - Aprime N FE 1 120.00 502.08 - Aprime N1 FE 1 120.00 502.08 - Aprime N2 FE 1 120.00 502.08 - Y R Y 1 105.40 1004.16 - Y A6 Y 1 124.50 502.08 - Y Aprime Y 1 124.50 502.08 - Y W Y 1 105.40 502.08 - FE W Y 1 127.30 502.08 - R Y A6 1 125.50 1004.16 - R Y Aprime 1 125.50 1004.16 - W Y A6 1 125.20 1004.16 - W Y Aprime 1 125.20 1004.16 - Z Y A6 1 124.20 1004.16 - Z Y Aprime 1 124.20 1004.16 - Z Y R 1 109.50 1004.16 - Z Y W 1 109.50 1004.16 - Y Z C2 1 125.40 502.08 - Y Z C3 1 125.40 502.08 - Y Z A6 1 124.40 1004.16 - Y Z Aprime 1 124.40 1004.16 - Z Z C2 1 127.50 502.08 - Z Z C3 1 127.50 502.08 - Z Z A6 1 128.40 1004.16 - Z Z Aprime 1 128.40 1004.16 - Z Z Y 1 107.00 1004.16 - Z C2 C1 1 109.50 502.08 - Z C2 C2 1 109.50 502.08 - Z C2 C3 1 109.50 502.08 - Z A6 A6 1 120.00 1004.16 - Z A6 A7 1 120.00 1004.16 - W FE N 1 90.00 502.08 - W FE N1 1 90.00 502.08 - W FE N2 1 90.00 502.08 - W FE W 1 180.00 502.08 - OF FE N 1 180.00 502.08 - OF FE N1 1 180.00 502.08 - OF FE N2 1 180.00 502.08 - OF FE W 1 90.00 502.08 - OF OF FE 1 120.00 502.08 - - -[ dihedraltypes ] -; Encad proper dihedrals. Note that there is a difference pf -; sign in the cosine definition between Gromacs and Encad. All angle values -; here are thus offset 180 degrees. - ; i l func q0 cq - C1 A6 A6 H 1 180.00 167.36 1 - C2 A6 A6 H 1 180.00 167.36 1 - C2 A5 A5 H 1 180.00 167.36 1 - C2 A5 A7 H 1 180.00 167.36 1 - C3 A6 A6 H 1 180.00 167.36 1 - C3 A7 A6 H 1 180.00 167.36 1 - C3 A7 A7 H 1 180.00 167.36 1 - C2 A5 A7 A6 1 180.00 167.36 1 - H A6 N C1 1 180.00 167.36 1 - A6 A6 A6 H 1 0.00 167.36 1 - L5 A7 A7 L5 1 0.00 167.36 1 - L5 A7 A7 L6 1 0.00 167.36 1 - L6 A7 A7 L6 1 0.00 167.36 1 - N A7 A6 A6 1 0.00 167.36 1 - N1 A7 A6 A6 1 0.00 167.36 1 - N2 A7 A6 A6 1 0.00 167.36 1 - N1 A7 A7 A6 1 0.00 167.36 1 - A6 A7 L5 A5 1 180.00 83.68 2 - A7 A7 N1 A5 1 180.00 167.36 1 - Aprime N C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N1 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N1 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N2 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp - Aprime N2 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp - HN N2 Aprime N2 1 180.00 41.84 2 ; not present in aanahn - C1 Aprime N C1 1 180.00 41.84 2 - C1 Aprime N C2 1 180.00 41.84 2 - C1 Aprime N C3 1 180.00 41.84 2 - C1 Aprime N1 C1 1 180.00 41.84 2 - C1 Aprime N1 C2 1 180.00 41.84 2 - C1 Aprime N1 C3 1 180.00 41.84 2 - C1 Aprime N2 C1 1 180.00 41.84 2 - C1 Aprime N2 C2 1 180.00 41.84 2 - C1 Aprime N2 C3 1 180.00 41.84 2 - C2 Aprime N C1 1 180.00 41.84 2 - C2 Aprime N C2 1 180.00 41.84 2 - C2 Aprime N C3 1 180.00 41.84 2 - C2 Aprime N1 C1 1 180.00 41.84 2 - C2 Aprime N1 C2 1 180.00 41.84 2 - C2 Aprime N1 C3 1 180.00 41.84 2 - C2 Aprime N2 C1 1 180.00 41.84 2 - C2 Aprime N2 C2 1 180.00 41.84 2 - C2 Aprime N2 C3 1 180.00 41.84 2 - C3 Aprime N C1 1 180.00 41.84 2 - C3 Aprime N C2 1 180.00 41.84 2 - C3 Aprime N C3 1 180.00 41.84 2 - C3 Aprime N1 C1 1 180.00 41.84 2 - C3 Aprime N1 C2 1 180.00 41.84 2 - C3 Aprime N1 C3 1 180.00 41.84 2 - C3 Aprime N2 C1 1 180.00 41.84 2 - C3 Aprime N2 C2 1 180.00 41.84 2 - C3 Aprime N2 C3 1 180.00 41.84 2 - C1 Aprime N1 HN 1 180.00 41.84 2 - C1 Aprime N2 HN 1 180.00 41.84 2 - C2 Aprime N1 HN 1 180.00 41.84 2 - C2 Aprime N2 HN 1 180.00 41.84 2 - C3 Aprime N1 HN 1 180.00 41.84 2 - C3 Aprime N2 HN 1 180.00 41.84 2 - C1 A6 A6 A6 1 0.00 334.72 1 - C2 A6 A6 A6 1 0.00 334.72 1 - C3 A6 A6 A6 1 0.00 334.72 1 - A6 A6 A6 A6 1 180.00 334.72 1 - N C1 CP CP 1 180.00 41.84 1 - N1 C1 CP CP 1 180.00 41.84 1 - N2 C1 CP CP 1 180.00 41.84 1 - C1 Aprime N CP 1 180.00 41.84 2 - C2 Aprime N CP 1 180.00 41.84 2 - C3 Aprime N CP 1 180.00 41.84 2 - Aprime N CP CP 1 0.00 41.84 1 - C1 A6 A6 X 1 180.00 41.84 2 - C2 A6 A6 X 1 180.00 41.84 2 - C2 A5 A5 X 1 180.00 41.84 2 - C2 A5 A7 X 1 180.00 41.84 2 - C3 A6 A6 X 1 180.00 41.84 2 - C3 A7 A6 X 1 180.00 41.84 2 - C3 A7 A7 X 1 180.00 41.84 2 - X A5 N C1 1 0.00 167.36 1 - X A5 N C2 1 0.00 167.36 1 - X A5 N C3 1 0.00 167.36 1 - X A5 N1 C1 1 0.00 167.36 1 - X A5 N1 C2 1 0.00 167.36 1 - X A5 N1 C3 1 0.00 167.36 1 - X A5 N2 C1 1 0.00 167.36 1 - X A5 N2 C2 1 0.00 167.36 1 - X A5 N2 C3 1 0.00 167.36 1 - C2 A5 N1 X 1 0.00 167.36 1 - X A6 N C1 1 0.00 167.36 1 - X A6 N C2 1 0.00 167.36 1 - X A6 N C3 1 0.00 167.36 1 - X A7 N C1 1 180.00 167.36 1 - X A7 N C2 1 180.00 167.36 1 - X A7 N C3 1 180.00 167.36 1 - X A7 N1 C1 1 180.00 167.36 1 - X A7 N1 C2 1 180.00 167.36 1 - X A7 N1 C3 1 180.00 167.36 1 - X A7 N2 C1 1 180.00 167.36 1 - X A7 N2 C2 1 180.00 167.36 1 - X A7 N2 C3 1 180.00 167.36 1 - S S C2 X 1 0.00 0.00 0 ; will be removed by grompp - X A6 A6 X 1 180.00 167.36 1 - X A6 A7 X 1 180.00 167.36 1 - X A5 A5 X 1 180.00 167.36 1 - X A5 A7 X 1 180.00 167.36 1 - X A7 A7 X 1 180.00 167.36 1 - X A5 N X 1 180.00 334.72 2 - X A5 N1 X 1 180.00 334.72 2 - X A5 N2 X 1 180.00 334.72 2 - X A5 L5 X 1 180.00 41.84 2 - X A6 N X 1 180.00 167.36 1 - X A6 N1 X 1 180.00 167.36 1 - X A6 N2 X 1 180.00 167.36 1 - X A6 L5 X 1 180.00 167.36 1 - X A6 L6 X 1 180.00 167.36 1 - X A7 L5 X 1 180.00 167.36 1 - X A7 L6 X 1 180.00 167.36 1 - X P O2 X 1 0.00 8.368 3 - X P OP X 1 0.00 8.368 3 - X N C1 X 1 0.00 0.00 0 ; will be removed by grompp - X N C2 X 1 0.00 0.00 0 ; will be removed by grompp - X N C3 X 1 0.00 0.00 0 ; will be removed by grompp - X N CP X 1 0.00 0.00 0 ; will be removed by grompp - X N1 C1 X 1 0.00 0.00 0 ; will be removed by grompp - X N1 C2 X 1 0.00 0.00 0 ; will be removed by grompp - X N1 C3 X 1 0.00 0.00 0 ; will be removed by grompp - X N1 CP X 1 0.00 0.00 0 ; will be removed by grompp - X N2 C1 X 1 0.00 0.00 0 ; will be removed by grompp - X N2 C2 X 1 0.00 0.00 0 ; will be removed by grompp - X N2 C3 X 1 0.00 0.00 0 ; will be removed by grompp - X N2 CP X 1 0.00 0.00 0 ; will be removed by grompp - X C1 O X 1 0.00 2.5104 3 - X C1 OH X 1 0.00 2.5104 3 - X C2 OH X 1 0.00 2.5104 3 - X C2 O2 X 1 0.00 2.5104 3 - X C2 OR X 1 0.00 2.5104 3 - X C3 OH X 1 0.00 2.5104 3 - X C1 C1 X 1 0.00 5.8576 3 - X C1 C2 X 1 0.00 5.8576 3 - X C1 C3 X 1 0.00 5.8576 3 - X C2 C2 X 1 0.00 5.8576 3 - X C2 C3 X 1 0.00 5.8576 3 - X C3 C3 X 1 0.00 5.8576 3 - X C1 CP X 1 180.00 5.8576 3 - X CP CP X 1 180.00 5.8576 3 - X C1 Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X C2 Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X C3 Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X CP Aprime X 1 0.00 0.00 0 ; will be removed by grompp - X C1 A6 X 1 0.00 0.4184 6 - X C1 A5 X 1 0.00 0.4184 6 - X C1 A7 X 1 0.00 0.4184 6 - X C1 Abis X 1 0.00 0.4184 6 - X C2 A6 X 1 0.00 0.4184 6 - X C2 A5 X 1 0.00 0.4184 6 - X C2 A7 X 1 0.00 0.4184 6 - X C2 Abis X 1 0.00 0.4184 6 - X C3 A6 X 1 0.00 0.4184 6 - X C3 A5 X 1 0.00 0.4184 6 - X C3 A7 X 1 0.00 0.4184 6 - X C3 Abis X 1 0.00 0.4184 6 - X C1 M3 X 1 0.00 5.8576 3 - X C2 M3 X 1 0.00 5.8576 3 - X C3 M3 X 1 0.00 5.8576 3 - X A6 O2 X 1 0.00 2.5104 3 - X Aprime OH X 1 0.00 2.5104 3 - X A6 OH X 1 0.00 2.5104 3 - X A6 M1 X 1 180.00 41.84 2 - X A6 M2 X 1 180.00 41.84 2 - X A6 M3 X 1 180.00 41.84 2 - X S C2 X 1 0.00 4.184 3 - X S C3 X 1 0.00 4.184 3 - X SH C2 X 1 0.00 4.184 3 - X S S X 1 0.00 25.104 2 - X M1 C1 X 1 0.00 5.8576 3 - X M1 C2 X 1 0.00 5.8576 3 - X M1 C3 X 1 0.00 5.8576 3 - X M2 C1 X 1 0.00 5.8576 3 - X M2 C2 X 1 0.00 5.8576 3 - X M2 C3 X 1 0.00 5.8576 3 - X Y A6 X 1 180.00 41.84 2 - X Y Aprime X 1 180.00 41.84 2 - X Y R X 1 180.00 83.68 2 - X Y W X 1 180.00 83.68 2 - X Z C2 X 1 0.00 0.4184 6 - X Z C3 X 1 0.00 0.4184 6 - X Z A6 X 1 180.00 41.84 2 - X Z Aprime X 1 180.00 41.84 2 - X Z Y X 1 180.00 83.68 2 - X Z Z X 1 180.00 83.68 2 - X FE N X 1 0.00 0.00 0 ; will be removed by grompp - X FE N1 X 1 0.00 0.00 0 ; will be removed by grompp - X FE N2 X 1 0.00 0.00 0 ; will be removed by grompp - X FE W X 1 0.00 0.00 0 ; will be removed by grompp - X OF FE X 1 0.00 0.00 0 ; will be removed by grompp - - - -; Encad out-of-plane potentials are the same functional form as -; Gromacs proper dihedrals (i.e. cosine, but with shifted sign). -; Note that the atom order is different too; In Gromacs, the first atom -; of an improper is the center one, while it is the 3rd in Encad. - -; Since they use the same type as proper dihedrals we use defines here -; to avoid mistakes in ambiguous cases. -; -; Note: the three parameters are repeated, to avoid having the free energy B state -; picked up from the default proper dihedral parameter types -; (grompp would give errors about non-matching multiplicity between A/B states) -; -; DNA -#define improper_X_X_P_X 180.0 8.368 3 180.0 8.368 3 -#define improper_X_X_M2_X 180.0 8.368 2 180.0 8.368 2 -; Proteins -#define improper_X_X_N_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_C_X 180.0 8.368 3 180.0 8.368 3 -#define improper_X_X_A_X 180.0 8.368 2 180.0 8.368 2 -#define improper_A_X_C1_X 60.0 75.312 1 60.0 75.312 1 -#define improper_A_X_C1_H -60.0 75.312 1 -60.0 75.312 1 -#define improper_X_X_C1_A 60.0 75.312 1 60.0 75.312 1 -#define improper_C3_C2_C1_C3 60.0 75.312 1 60.0 75.312 1 -#define improper_C_C1_C1_C3 60.0 75.312 1 60.0 75.312 1 -#define improper_C3_C1_C1_OH -60.0 75.312 1 -60.0 75.312 1 -#define improper_C1_C2_C1_C3 -60.0 75.312 1 -60.0 75.312 1 -#define improper_N_A_C1_C -60.0 75.312 1 -60.0 75.312 1 -#define improper_M_A_C1_C -60.0 75.312 1 -60.0 75.312 1 -#define improper_X_X_M_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_M3_X 180.0 8.368 3 180.0 8.368 3 -; Heme -#define improper_X_X_R_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_W_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_Y_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_Z_X 180.0 8.368 2 180.0 8.368 2 -#define improper_X_X_FE_X 180.0 0.000 4 180.0 0.000 4 -#define improper_X_X_OF_X 180.0 8.368 2 180.0 8.368 2 - - - diff --git a/share/top/encadv.ff/ffnonbonded.itp b/share/top/encadv.ff/ffnonbonded.itp deleted file mode 100644 index 12ccbe18d3..0000000000 --- a/share/top/encadv.ff/ffnonbonded.itp +++ /dev/null @@ -1,55 +0,0 @@ -[ atomtypes ] -;name at.num mass charge ptype sigma epsilon - H 1 1.008 0.0 A 2.54129e-01 1.58992e-01 - O 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - N 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - N1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - N2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - C1 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - C2 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - C3 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - CP 6 12.011 0.0 A 3.84423e-01 3.08863e-01 - A6 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - A5 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - A7 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - Aprime 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - Abis 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - L5 7 14.0027 0.0 A 2.76223e-01 7.73161e-01 - L6 7 14.0027 0.0 A 2.76223e-01 7.73161e-01 - P 15 30.9738 0.0 A 3.84423e-01 3.08863e-01 - OH 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - O2 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - OR 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - S 16 32.060 0.0 A 3.84423e-01 3.08863e-01 - SH 16 32.060 0.0 A 3.84423e-01 3.08863e-01 - M1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - M2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - M3 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - HN 1 1.008 0.0 A 4.45449e-02 4.18400e-02 - HO 1 1.008 0.0 A 4.45449e-02 4.18400e-02 - HW 1 1.008 0.0 A 4.45449e-02 4.18400e-02 - CL 17 35.453 0.0 A 4.31068e-01 3.51456e-01 - Obis 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - OP 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - R 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - W 7 14.0027 0.0 A 3.40065e-01 1.72862e+00 - Y 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - Z 6 12.011 0.0 A 3.75977e-01 1.57444e-01 - FE 26 55.847 0.0 A 3.84423e-01 3.08863e-01 - OF 8 15.9994 0.0 A 2.76223e-01 7.73161e-01 - OW 8 15.9994 0.0 A 3.16556e-01 7.73161e-01 - AR 18 39.948 0.0 A 2.54129e-01 1.58992e-01 - NA 11 22.9898 0.0 A 2.40543e-01 7.73161e-01 - MCH3 0 0.0 0.0 A 0.0 0.0 - MNH3 0 0.0 0.0 A 0.0 0.0 - MW 0 0.0 0.0 D 0.0 0.0 - -[ nonbond_params ] - ; i j func c6 c12 -; Encad uses strict combination rules, so no need for explicit parameters - -[ pairtypes ] - ; i j func cs6 cs12 -; 1,4 interactions are calculated automatically, using fudge factors. -; (In the current version, the factors are 0.0, meaning no 1,4 interactions). - diff --git a/share/top/encadv.ff/forcefield.doc b/share/top/encadv.ff/forcefield.doc deleted file mode 100644 index 778b023fb8..0000000000 --- a/share/top/encadv.ff/forcefield.doc +++ /dev/null @@ -1 +0,0 @@ -[DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges diff --git a/share/top/encadv.ff/forcefield.itp b/share/top/encadv.ff/forcefield.itp deleted file mode 100644 index bfcbe0b23a..0000000000 --- a/share/top/encadv.ff/forcefield.itp +++ /dev/null @@ -1,19 +0,0 @@ -#define _FF_ENCAD -; Implemented from encad library version 25/xi/91, -; with 1,4 interaction setup modified by Michael Levitt. -; In this forcefield, both coulombic and Lennard-Jones interactions -; are completely excluded for 1,4 interaction sites. -; -; Vacuum version - scaled down charges. - -; -[ defaults ] -; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ - 1 3 yes 0.0 0.0 - -#include "ffnonbonded.itp" -#include "ffbonded.itp" - - - - diff --git a/share/top/encadv.ff/watermodels.dat b/share/top/encadv.ff/watermodels.dat deleted file mode 100644 index 592e150e5f..0000000000 --- a/share/top/encadv.ff/watermodels.dat +++ /dev/null @@ -1 +0,0 @@ -f3c F3C flexible three-centered water model diff --git a/share/top/ffencads.itp b/share/top/ffencads.itp deleted file mode 100644 index dc53c355ac..0000000000 --- a/share/top/ffencads.itp +++ /dev/null @@ -1,3 +0,0 @@ -; This file is for backward compatibility only. -; Please directly include the file below in your .top file. -#include "encads.ff/forcefield.itp" diff --git a/share/top/ffencadv.itp b/share/top/ffencadv.itp deleted file mode 100644 index 10022f230a..0000000000 --- a/share/top/ffencadv.itp +++ /dev/null @@ -1,3 +0,0 @@ -; This file is for backward compatibility only. -; Please directly include the file below in your .top file. -#include "encadv.ff/forcefield.itp"