From 05d7d98932b91f4821b8619e3cadc5b921c02215 Mon Sep 17 00:00:00 2001 From: Berk Hess Date: Thu, 7 May 2015 10:01:26 +0200 Subject: [PATCH] Removed non-ff atomtypes from oplsaa and charmm27 Removed atom types Cu2+, Fe2+ and SI from oplsaa and charmm27, since they are not part of the official force fields. Refs #957. Change-Id: Ic8ebdbee62b4441184a54a580b83849ba21ca978 --- share/top/charmm27.ff/ffnonbonded.itp | 5 ----- share/top/oplsaa.ff/aminoacids.rtp | 9 +-------- share/top/oplsaa.ff/atomtypes.atp | 6 ------ share/top/oplsaa.ff/ffbonded.itp | 22 ---------------------- share/top/oplsaa.ff/ffnonbonded.itp | 6 ------ share/top/oplsaa.ff/ions.itp | 8 -------- 6 files changed, 1 insertion(+), 55 deletions(-) diff --git a/share/top/charmm27.ff/ffnonbonded.itp b/share/top/charmm27.ff/ffnonbonded.itp index 82daff2332..34323decbd 100644 --- a/share/top/charmm27.ff/ffnonbonded.itp +++ b/share/top/charmm27.ff/ffnonbonded.itp @@ -157,11 +157,6 @@ MNH2 0 0.000000 0.00 A 0.0 0.0 MCH3 0 0.000000 0.00 A 0.0 0.0 MCH3S 0 0.000000 0.00 A 0.0 0.0 MW 0 0.000000 0.00 A 0.0 0.0 -; Ions and noble gases (useful for tutorials) -Cu2+ 29 63.54600 2.00 A 2.08470e-01 4.76976e+00 -Ar 18 39.94800 0.00 A 3.41000e-01 2.74580e-02 -; Added by DvdS 05/2005 copied from GROMACS force field. -SI 14 28.08000 0.00 A 3.38550e-01 2.44704e+00 [ pairtypes ] ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS diff --git a/share/top/oplsaa.ff/aminoacids.rtp b/share/top/oplsaa.ff/aminoacids.rtp index abadb0b386..07869cb852 100644 --- a/share/top/oplsaa.ff/aminoacids.rtp +++ b/share/top/oplsaa.ff/aminoacids.rtp @@ -1590,14 +1590,6 @@ [ atoms ] BA opls_414 2.000 0 -; Metal ions -[ CU ] - [ atoms ] - CU Cu2+ 2.000 0 - -[ FE ] - [ atoms ] - FE Fe2+ 2.000 0 ; Ethanol - CA is the carbon bound to the OH group [ EtOH ] @@ -1621,6 +1613,7 @@ CA OH OH HO + ; New All atom DMSO model, DvdS, 17/06/2006 ; Use at your own risk! [ DMSO ] diff --git a/share/top/oplsaa.ff/atomtypes.atp b/share/top/oplsaa.ff/atomtypes.atp index ce255af96f..9a5d4a9eed 100644 --- a/share/top/oplsaa.ff/atomtypes.atp +++ b/share/top/oplsaa.ff/atomtypes.atp @@ -826,12 +826,6 @@ MCH3B 0.0 ; Dummy mass in rigid tetraedrical CH3 group MW 0.0 ; Dummy mass in rigid tyrosine rings DUM 0.0 ; Dummy mass in TIP4P etc. -; These ion atomtypes are NOT part of OPLS, but since they are -; needed for some proteins we have added them. - Cu2+ 63.546 ; Copper. See Inorg. Chem. 40, 5223 (2001). - Fe2+ 55.847 ; Iron. See Chem. Phys. Lett. 449, 144 (2007). -; Added by DvdS 05/2005 copied from GROMACS force field. - SI 28.080 ; Silicium in Glass etc. ; tip4p-EW HW_tip4pew 1.008 OW_tip4pew 16.00 diff --git a/share/top/oplsaa.ff/ffbonded.itp b/share/top/oplsaa.ff/ffbonded.itp index 357af4d8fd..907840488f 100644 --- a/share/top/oplsaa.ff/ffbonded.itp +++ b/share/top/oplsaa.ff/ffbonded.itp @@ -2666,28 +2666,6 @@ #define improper_Z_CA_X_Y 180.0 4.60240 2 -; -; This bit added by DvdS for quartz simulation 2005-05-07 -; These parameters are taken from GROMOS and were also used in -; Wensink et al. Langmuir 16 (2000) pp. 7392-7400 -; -[ bondtypes ] -; i j func b0 kb - SI OS 1 0.16300 251040. ; From GROMACS - SI OH 1 0.16300 251040. ; - -[ angletypes ] -; i j k func th0 cth - SI OS SI 1 155.000 397.480 - OS SI OS 1 109.500 397.480 - OH SI OS 1 109.500 397.480 - SI OH HO 1 109.500 397.480 - -[ dihedraltypes ] -; i j k l func coefficients -; Added DvdS for Quartz simulations - SI OS 1 0.000 3.766 3 - SI OH 1 0.000 3.766 3 ; Added by DvdS for DMSO 17/06/2006 [ bondtypes ] diff --git a/share/top/oplsaa.ff/ffnonbonded.itp b/share/top/oplsaa.ff/ffnonbonded.itp index 6887f656ee..20e5b31d95 100644 --- a/share/top/oplsaa.ff/ffnonbonded.itp +++ b/share/top/oplsaa.ff/ffnonbonded.itp @@ -823,12 +823,6 @@ 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 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 - Fe2+ Fe2+ 26 55.84700 2.000 A 2.59400e-01 5.43920e-02 -; Added by DvdS 05/2005 copied from GROMACS force field. - SI SI 14 28.08000 0.000 A 3.38550e-01 2.44704e+00 ; tip4p-EW HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 diff --git a/share/top/oplsaa.ff/ions.itp b/share/top/oplsaa.ff/ions.itp index 83c21cac87..b60240da7d 100644 --- a/share/top/oplsaa.ff/ions.itp +++ b/share/top/oplsaa.ff/ions.itp @@ -2,14 +2,6 @@ ; See literature references in forcefield.itp and atomtypes.atp ; -[ moleculetype ] -; molname nrexcl -CU 1 - -[ atoms ] -; id at type res nr residu name at name cg nr charge mass -1 Cu2+ 1 CU CU 1 2 63.54600 - [ moleculetype ] ; molname nrexcl MG 1 -- 2.22.0