From: David van der Spoel Date: Wed, 25 Sep 2013 12:00:31 +0000 (+0200) Subject: Made MW of the Vsite particle type. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=5132383c8d532c1bfebaab43c58cccd5ebfa54be;p=alexxy%2Fgromacs.git Made MW of the Vsite particle type. grompp checks whether particles that are not shells or vsites have a positive mass. Since MW is used in TIP4P etc. as a massless particle it should have the appropriate particle type. Change-Id: I45d0af3230949be8b07a45d131bc10d9d39d945e --- diff --git a/share/top/amber03.ff/ffnonbonded.itp b/share/top/amber03.ff/ffnonbonded.itp index 24e54031e0..c2e051fb92 100644 --- a/share/top/amber03.ff/ffnonbonded.itp +++ b/share/top/amber03.ff/ffnonbonded.itp @@ -70,7 +70,7 @@ HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 ; dummy defs ; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00 ; Dummy masses for rigid CH3 and NH3 groups MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber94.ff/ffnonbonded.itp b/share/top/amber94.ff/ffnonbonded.itp index ef3fde6d98..8eca3cf132 100644 --- a/share/top/amber94.ff/ffnonbonded.itp +++ b/share/top/amber94.ff/ffnonbonded.itp @@ -69,7 +69,7 @@ HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 ; dummy defs ; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00 ; Dummy masses for rigid CH3 and NH3 groups MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber96.ff/ffnonbonded.itp b/share/top/amber96.ff/ffnonbonded.itp index ef3fde6d98..8eca3cf132 100644 --- a/share/top/amber96.ff/ffnonbonded.itp +++ b/share/top/amber96.ff/ffnonbonded.itp @@ -69,7 +69,7 @@ HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 ; dummy defs ; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00 ; Dummy masses for rigid CH3 and NH3 groups MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber99.ff/ffnonbonded.itp b/share/top/amber99.ff/ffnonbonded.itp index ef3fde6d98..8eca3cf132 100644 --- a/share/top/amber99.ff/ffnonbonded.itp +++ b/share/top/amber99.ff/ffnonbonded.itp @@ -69,7 +69,7 @@ HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 ; dummy defs ; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00 ; Dummy masses for rigid CH3 and NH3 groups MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber99sb-ildn.ff/ffnonbonded.itp b/share/top/amber99sb-ildn.ff/ffnonbonded.itp index ef3fde6d98..8eca3cf132 100644 --- a/share/top/amber99sb-ildn.ff/ffnonbonded.itp +++ b/share/top/amber99sb-ildn.ff/ffnonbonded.itp @@ -69,7 +69,7 @@ HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 ; dummy defs ; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00 ; Dummy masses for rigid CH3 and NH3 groups MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber99sb.ff/ffnonbonded.itp b/share/top/amber99sb.ff/ffnonbonded.itp index ef3fde6d98..8eca3cf132 100644 --- a/share/top/amber99sb.ff/ffnonbonded.itp +++ b/share/top/amber99sb.ff/ffnonbonded.itp @@ -69,7 +69,7 @@ HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 ; dummy defs ; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00 ; Dummy masses for rigid CH3 and NH3 groups MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amberGS.ff/ffnonbonded.itp b/share/top/amberGS.ff/ffnonbonded.itp index ef3fde6d98..8eca3cf132 100644 --- a/share/top/amberGS.ff/ffnonbonded.itp +++ b/share/top/amberGS.ff/ffnonbonded.itp @@ -69,7 +69,7 @@ HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 ; dummy defs ; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00 ; Dummy masses for rigid CH3 and NH3 groups MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/charmm27.ff/ffnonbonded.itp b/share/top/charmm27.ff/ffnonbonded.itp index 41a6f2058c..48ab6326d3 100644 --- a/share/top/charmm27.ff/ffnonbonded.itp +++ b/share/top/charmm27.ff/ffnonbonded.itp @@ -133,10 +133,10 @@ OWT3 8 9.951400 -0.834 A 3.15058e-01 6.36386e-01 ; TIP3p O HWT3 1 4.032000 0.417 A 0.0 0.0 ; TIP3p H OWT4 8 9.951400 0.0 A 3.15365e-01 6.48520e-01 ; TIP4p O HWT4 1 4.032000 0.52 A 0.0 0.0 ; TIP4p H -MWT4 0 0.000000 -1.04 A 0.0 0.0 ; TIP4p vsite +MWT4 0 0.000000 -1.04 D 0.0 0.0 ; TIP4p vsite OWT5 8 9.951400 0.0 A 3.12000e-01 6.69440e-01 ; TIP5p O HWT5 1 4.032000 0.241 A 0.0 0.0 ; TIP5p H -MWT5 0 0.000000 -0.241 A 0.0 0.0 ; TIP5p vsite +MWT5 0 0.000000 -0.241 D 0.0 0.0 ; TIP5p vsite OW 8 9.951400 -0.82 A 3.16557e-01 6.50194e-01 ; SPC 0 HW 1 4.032000 0.41 A 0.0 0.0; SPC H #else @@ -144,10 +144,10 @@ OWT3 8 15.999400 -0.834 A 3.15058e-01 6.36386e-01 ; TIP3p O HWT3 1 1.008000 0.417 A 0.0 0.0 ; TIP3p H OWT4 8 15.999400 0.0 A 3.15365e-01 6.48520e-01 ; TIP4p O HWT4 1 1.008000 0.52 A 0.0 0.0 ; TIP4p H -MWT4 0 0.000000 -1.04 A 0.0 0.0 ; TIP4p vsite +MWT4 0 0.000000 -1.04 D 0.0 0.0 ; TIP4p vsite OWT5 8 15.999400 0.0 A 3.12000e-01 6.69440e-01 ; TIP5p O HWT5 1 1.008000 0.241 A 0.0 0.0 ; TIP5p H -MWT5 0 0.000000 -0.241 A 0.0 0.0 ; TIP5p vsite +MWT5 0 0.000000 -0.241 D 0.0 0.0 ; TIP5p vsite OW 8 15.999400 -0.82 A 3.16557e-01 6.50194e-01 ; SPC O HW 1 1.008000 0.41 A 0.0 0.0 ; SPC H #endif diff --git a/share/top/encads.ff/ffnonbonded.itp b/share/top/encads.ff/ffnonbonded.itp index 22b8cca173..4081f3eae8 100644 --- a/share/top/encads.ff/ffnonbonded.itp +++ b/share/top/encads.ff/ffnonbonded.itp @@ -42,7 +42,7 @@ 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 A 0.0 0.0 + MW 0 0.0 0.0 D 0.0 0.0 [ nonbond_params ] ; i j func c6 c12 diff --git a/share/top/encadv.ff/ffnonbonded.itp b/share/top/encadv.ff/ffnonbonded.itp index 6042e7cdf4..12ccbe18d3 100644 --- a/share/top/encadv.ff/ffnonbonded.itp +++ b/share/top/encadv.ff/ffnonbonded.itp @@ -42,7 +42,7 @@ 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 A 0.0 0.0 + MW 0 0.0 0.0 D 0.0 0.0 [ nonbond_params ] ; i j func c6 c12 diff --git a/share/top/gmx.ff/ffnonbonded.itp b/share/top/gmx.ff/ffnonbonded.itp index e1d01fe915..a84979a8f0 100644 --- a/share/top/gmx.ff/ffnonbonded.itp +++ b/share/top/gmx.ff/ffnonbonded.itp @@ -59,8 +59,8 @@ CD 6 15.03500 0.000 A 0.90507E-02 0.21758E-04 CHE 6 12.01100 0.000 A 0.23402E-02 0.33740E-05 MNH3 0 0.0 0.000 A 0.0 0.0 - MW 0 0.0 0.000 A 0.0 0.0 - DUM 0 0.0 0.000 A 0.0 0.0 + MW 0 0.0 0.000 D 0.0 0.0 + DUM 0 0.0 0.000 D 0.0 0.0 IW 0 0.0 0.000 D 0.0 0.0 [ nonbond_params ] diff --git a/share/top/gmx2.ff/ffnonbonded.itp b/share/top/gmx2.ff/ffnonbonded.itp index ad2afa69fa..071a275c6e 100644 --- a/share/top/gmx2.ff/ffnonbonded.itp +++ b/share/top/gmx2.ff/ffnonbonded.itp @@ -60,7 +60,7 @@ CHE 6 12.01100 0.000 A 0.23402E-02 0.33740E-05 MNH3 0 0.0 0.000 A 0.0 0.0 MCH3 0 0.0 0.000 A 0.0 0.0 - MW 0 0.0 0.000 A 0.0 0.0 + MW 0 0.0 0.000 D 0.0 0.0 [ nonbond_params ] ; i j func c6 c12 diff --git a/share/top/gromos43a1.ff/ffnonbonded.itp b/share/top/gromos43a1.ff/ffnonbonded.itp index eb5c995afe..3e49942980 100644 --- a/share/top/gromos43a1.ff/ffnonbonded.itp +++ b/share/top/gromos43a1.ff/ffnonbonded.itp @@ -46,8 +46,8 @@ CLCl4 17 0.000 0.000 A 0.0076040144 1.2767758e-05 MNH3 0 0.000 0.000 A 0.0 0.0 OWT3 8 15.9994 0.000 A 0.24889E-02 0.24352E-05 OWT4 8 15.9994 0.000 A 0.25519e-02 0.25104e-05 - MW 0 0.000 0.000 A 0.0 0.0 - DUM 0 0.000 0.000 A 0.0 0.0 + MW 0 0.000 0.000 D 0.0 0.0 + DUM 0 0.000 0.000 D 0.0 0.0 IW 0 0.000 0.000 D 0.0 0.0 [ nonbond_params ] diff --git a/share/top/gromos43a2.ff/ffnonbonded.itp b/share/top/gromos43a2.ff/ffnonbonded.itp index 1eaed13fe8..3e898a819a 100644 --- a/share/top/gromos43a2.ff/ffnonbonded.itp +++ b/share/top/gromos43a2.ff/ffnonbonded.itp @@ -46,8 +46,8 @@ CLCl4 17 0.000 0.000 A 0.0076040144 1.2767758e-05 MNH3 0 0.000 0.000 A 0.0 0.0 OWT3 8 15.9994 0.000 A 0.24889E-02 0.24352E-05 OWT4 8 15.9994 0.000 A 0.25519e-02 0.25104e-05 - MW 0 0.000 0.000 A 0.0 0.0 - DUM 0 0.000 0.000 A 0 0 + MW 0 0.000 0.000 D 0.0 0.0 + DUM 0 0.000 0.000 D 0 0 IW 0 0.000 0.000 D 0 0 LA 0 0.000 0.000 A 0 0 XX 0 0.000 0.000 A 0 0 diff --git a/share/top/gromos45a3.ff/ffnonbonded.itp b/share/top/gromos45a3.ff/ffnonbonded.itp index 9ba98bb4bb..93f6ae843f 100644 --- a/share/top/gromos45a3.ff/ffnonbonded.itp +++ b/share/top/gromos45a3.ff/ffnonbonded.itp @@ -47,7 +47,7 @@ CLCl4 17 0.000 0.000 A 0.0076040144 1.2767758e-05 CH0 6 0.000 0.000 A 0.0023970816 0.0002053489 SI 14 0.000 0.000 A 0.01473796 2.2193521e-05 MNH3 0 0.000 0.000 A 0.0 0.0 - MW 0 0.000 0.000 A 0.0 0.0 + MW 0 0.000 0.000 D 0.0 0.0 [ nonbond_params ] ; i j func c6 c12 diff --git a/share/top/gromos53a5.ff/ffnonbonded.itp b/share/top/gromos53a5.ff/ffnonbonded.itp index 2c1b232b4c..9f1426ce06 100644 --- a/share/top/gromos53a5.ff/ffnonbonded.itp +++ b/share/top/gromos53a5.ff/ffnonbonded.itp @@ -55,7 +55,7 @@ OUrea 8 0.000 0.000 A 0.0023639044 1.5898688e-06 NUrea 7 0.000 0.000 A 0.0033527574 3.9509513e-06 SI 14 0.000 0.000 A 0.01473796 2.2193521e-05 MNH3 0 0.000 0.000 A 0.0 0.0 - MW 0 0.000 0.000 A 0.0 0.0 + MW 0 0.000 0.000 D 0.0 0.0 [ nonbond_params ] ; i j func c6 c12 diff --git a/share/top/gromos53a6.ff/ffnonbonded.itp b/share/top/gromos53a6.ff/ffnonbonded.itp index 7257b90502..22148eb558 100644 --- a/share/top/gromos53a6.ff/ffnonbonded.itp +++ b/share/top/gromos53a6.ff/ffnonbonded.itp @@ -55,7 +55,7 @@ OUrea 8 0.000 0.000 A 0.0023639044 1.5898688e-06 NUrea 7 0.000 0.000 A 0.0033527574 3.9509513e-06 SI 14 0.000 0.000 A 0.01473796 2.2193521e-05 MNH3 0 0.000 0.000 A 0.0 0.0 - MW 0 0.000 0.000 A 0.0 0.0 + MW 0 0.000 0.000 D 0.0 0.0 [ nonbond_params ] ; i j func c6 c12 diff --git a/share/top/gromos54a7.ff/ffnonbonded.itp b/share/top/gromos54a7.ff/ffnonbonded.itp index 624a2c95a1..896450ffad 100644 --- a/share/top/gromos54a7.ff/ffnonbonded.itp +++ b/share/top/gromos54a7.ff/ffnonbonded.itp @@ -55,7 +55,7 @@ OUrea 8 0.000 0.000 A 0.0023639044 1.5898688e-06 NUrea 7 0.000 0.000 A 0.0033527574 3.9509513e-06 SI 14 0.000 0.000 A 0.01473796 2.2193521e-05 MNH3 0 0.000 0.000 A 0.0 0.0 - MW 0 0.000 0.000 A 0.0 0.0 + MW 0 0.000 0.000 D 0.0 0.0 CH3p 6 0.000 0.000 A 0.0096138025 2.6646244e-05 [ nonbond_params ] diff --git a/share/top/oplsaa.ff/ffnonbonded.itp b/share/top/oplsaa.ff/ffnonbonded.itp index 124b1de91b..cfc48092c0 100644 --- a/share/top/oplsaa.ff/ffnonbonded.itp +++ b/share/top/oplsaa.ff/ffnonbonded.itp @@ -821,7 +821,7 @@ MNH2 MNH2 0 0.00000 0.000 A 0.00000e+00 0.00000e+00 MCH3A MCH3A 0 0.00000 0.000 A 0.00000e+00 0.00000e+00 MCH3B MCH3B 0 0.00000 0.000 A 0.00000e+00 0.00000e+00 - MW MW 0 0.00000 0.000 A 0.00000e+00 0.00000e+00 + MW MW 0 0.00000 0.000 D 0.00000e+00 0.00000e+00 ; These ion atomtypes are NOT part of OPLS, but since they are ; needed for some proteins. Cu2+ Cu2+ 29 63.54600 2.000 A 2.08470e-01 4.76976e+00