diff --git a/test-charmm-build/1A25/parameters b/test-charmm-build/1A25/parameters index f667868..6dc1448 100644 --- a/test-charmm-build/1A25/parameters +++ b/test-charmm-build/1A25/parameters @@ -5,7 +5,7 @@ * All comments to the CHARMM web site: www.charmm.org * parameter set discussion forum * -! + !references ! !Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M, de Groot, B.L., @@ -32,169 +32,169 @@ !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. -! + * Parameters for water and ions * -! -! + + * par_cation.prm for mono-, di-, and trivalent cations * -! -!ATOMS + +ATOMS !Following lines added from par_all36m_prot.prm -!MASS -1 H 1.00800 ! polar H -!MASS -1 HC 1.00800 ! N-ter H -!MASS -1 HA 1.00800 ! nonpolar H -!MASS -1 HP 1.00800 ! aromatic H -!MASS -1 HB1 1.00800 ! backbone H -!MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 -!MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 -!MASS -1 HR2 1.00800 ! (+) his HE1 -!MASS -1 HR3 1.00800 ! neutral his HG, HD2 -!MASS -1 HS 1.00800 ! thiol hydrogen -!MASS -1 HE1 1.00800 ! for alkene; RHC=CR -!MASS -1 HE2 1.00800 ! for alkene; H2C=CR -!MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 C 12.01100 ! carbonyl C, peptide backbone -!MASS -1 CA 12.01100 ! aromatic C -!MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters -!MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH -!MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 -!MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu -!MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 -!MASS -1 CPH1 12.01100 ! his CG and CD2 carbons -!MASS -1 CPH2 12.01100 ! his CE1 carbon -!MASS -1 CPT 12.01100 ! trp C between rings -!MASS -1 CY 12.01100 ! TRP C in pyrrole ring -!MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) -!MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) -!MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) -!MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 -!MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 -!MASS -1 CS 12.01100 ! thiolate carbon -!MASS -1 CE1 12.01100 ! for alkene; RHC=CR -!MASS -1 CE2 12.01100 ! for alkene; H2C=CR -!MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp -!MASS -1 C3 12.01100 ! cyclopropane carbon -!MASS -1 N 14.00700 ! proline N -!MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen -!MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen -!MASS -1 NR3 14.00700 ! charged his ring nitrogen -!MASS -1 NH1 14.00700 ! peptide nitrogen -!MASS -1 NH2 14.00700 ! amide nitrogen -!MASS -1 NH3 14.00700 ! ammonium nitrogen -!MASS -1 NC2 14.00700 ! guanidinium nitrogen -!MASS -1 NY 14.00700 ! TRP N in pyrrole ring -!MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) -!MASS -1 O 15.99900 ! carbonyl oxygen -!MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid -!MASS -1 OC 15.99900 ! carboxylate oxygen -!MASS -1 OH1 15.99900 ! hydroxyl oxygen -!MASS -1 OS 15.99940 ! ester oxygen -!MASS -1 S 32.06000 ! sulphur -!MASS -1 SM 32.06000 ! sulfur C-S-S-C type -!MASS -1 SS 32.06000 ! thiolate sulfur -! -! +MASS -1 H 1.00800 ! polar H +MASS -1 HC 1.00800 ! N-ter H +MASS -1 HA 1.00800 ! nonpolar H +MASS -1 HP 1.00800 ! aromatic H +MASS -1 HB1 1.00800 ! backbone H +MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS -1 HR2 1.00800 ! (+) his HE1 +MASS -1 HR3 1.00800 ! neutral his HG, HD2 +MASS -1 HS 1.00800 ! thiol hydrogen +MASS -1 HE1 1.00800 ! for alkene; RHC=CR +MASS -1 HE2 1.00800 ! for alkene; H2C=CR +MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 C 12.01100 ! carbonyl C, peptide backbone +MASS -1 CA 12.01100 ! aromatic C +MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters +MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH +MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu +MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS -1 CPH1 12.01100 ! his CG and CD2 carbons +MASS -1 CPH2 12.01100 ! his CE1 carbon +MASS -1 CPT 12.01100 ! trp C between rings +MASS -1 CY 12.01100 ! TRP C in pyrrole ring +MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) +MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) +MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS -1 CS 12.01100 ! thiolate carbon +MASS -1 CE1 12.01100 ! for alkene; RHC=CR +MASS -1 CE2 12.01100 ! for alkene; H2C=CR +MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp +MASS -1 C3 12.01100 ! cyclopropane carbon +MASS -1 N 14.00700 ! proline N +MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS -1 NR3 14.00700 ! charged his ring nitrogen +MASS -1 NH1 14.00700 ! peptide nitrogen +MASS -1 NH2 14.00700 ! amide nitrogen +MASS -1 NH3 14.00700 ! ammonium nitrogen +MASS -1 NC2 14.00700 ! guanidinium nitrogen +MASS -1 NY 14.00700 ! TRP N in pyrrole ring +MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS -1 O 15.99900 ! carbonyl oxygen +MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS -1 OC 15.99900 ! carboxylate oxygen +MASS -1 OH1 15.99900 ! hydroxyl oxygen +MASS -1 OS 15.99940 ! ester oxygen +MASS -1 S 32.06000 ! sulphur +MASS -1 SM 32.06000 ! sulfur C-S-S-C type +MASS -1 SS 32.06000 ! thiolate sulfur + + !Following lines added from par_water_ions.prm -!MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN -!MASS -1 HX 1.00800 ! hydroxide hydrogen -!MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN -!MASS -1 OX 15.99940 ! hydroxide oxygen -!MASS -1 HPER 1.00800 ! H of H2O2 -!MASS -1 OPER 15.99900 ! O of H2O2 -!MASS -1 LIT 6.94100 ! Lithium ion -!MASS -1 SOD 22.98977 ! Sodium Ion -!MASS -1 MG 24.30500 ! Magnesium Ion -!MASS -1 POT 39.09830 ! Potassium Ion -!MASS -1 CAL 40.08000 ! Calcium Ion -!MASS -1 RUB 85.46780 ! Rubidium Ion -!MASS -1 CES 132.90545 ! Cesium Ion -!MASS -1 BAR 137.32700 ! Barium Ion -!MASS -1 ZN 65.37000 ! zinc (II) cation -!MASS -1 CAD 112.41100 ! cadmium (II) cation -!MASS -1 CLA 35.45000 ! Chloride Ion -! +MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS -1 HX 1.00800 ! hydroxide hydrogen +MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS -1 OX 15.99940 ! hydroxide oxygen +MASS -1 HPER 1.00800 ! H of H2O2 +MASS -1 OPER 15.99900 ! O of H2O2 +MASS -1 LIT 6.94100 ! Lithium ion +MASS -1 SOD 22.98977 ! Sodium Ion +MASS -1 MG 24.30500 ! Magnesium Ion +MASS -1 POT 39.09830 ! Potassium Ion +MASS -1 CAL 40.08000 ! Calcium Ion +MASS -1 RUB 85.46780 ! Rubidium Ion +MASS -1 CES 132.90545 ! Cesium Ion +MASS -1 BAR 137.32700 ! Barium Ion +MASS -1 ZN 65.37000 ! zinc (II) cation +MASS -1 CAD 112.41100 ! cadmium (II) cation +MASS -1 CLA 35.45000 ! Chloride Ion + !Following lines added from par_all36_prot_arg0.prm -!MASS -1 HRA3 1.00800 ! alphatic proton, CH3 -!MASS -1 HRP2 1.00800 ! polar H, +ve charge -!MASS -1 HRM1 1.00800 ! polar H, dimethylamine -!MASS -1 HRM2 1.00800 ! polar H, methylamine -!MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium -!MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) -!MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base -!MASS -1 NRN1 14.00700 ! dimethylamine nitrogen -!MASS -1 NRN2 14.00700 ! methylamine nitrogen -! +MASS -1 HRA3 1.00800 ! alphatic proton, CH3 +MASS -1 HRP2 1.00800 ! polar H, +ve charge +MASS -1 HRM1 1.00800 ! polar H, dimethylamine +MASS -1 HRM2 1.00800 ! polar H, methylamine +MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium +MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) +MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base +MASS -1 NRN1 14.00700 ! dimethylamine nitrogen +MASS -1 NRN2 14.00700 ! methylamine nitrogen + !Following lines added from par_ions_won.prm !MASS -1 Li1p 6.94000 ! Lithium !MASS -1 Na1p 22.99000 ! Sodium !MASS -1 K1p 39.09000 ! Potassium !MASS -1 Rb1p 85.46000 ! Rubidium !MASS -1 Cs1p 132.91000 ! Cesium -!MASS -1 Cu1p 63.54600 ! Copper -!MASS -1 Ag1p 107.87000 ! Silver -!MASS -1 Au1p 196.97000 ! Gold -!MASS -1 Ti1p 47.86700 ! Titanium -!MASS -1 Be2p 9.01220 ! Beryllium +MASS -1 Cu1p 63.54600 ! Copper +MASS -1 Ag1p 107.87000 ! Silver +MASS -1 Au1p 196.97000 ! Gold +MASS -1 Ti1p 47.86700 ! Titanium +MASS -1 Be2p 9.01220 ! Beryllium !MASS -1 Mg2p 24.30500 ! Magnesium !MASS -1 Ca2p 40.07800 ! Calcium -!MASS -1 Sr2p 87.62000 ! Strontium +MASS -1 Sr2p 87.62000 ! Strontium !MASS -1 Ba2p 1 37.33 00 ! Barium -!MASS -1 Ra2p 226.03000 ! Radium -!MASS -1 V2p 50.94200 ! Vanadium -!MASS -1 Cr2p 51.99600 ! Chromium -!MASS -1 Mn2p 54.93800 ! Manganese -!MASS -1 Fe2p 55.85400 ! Iron -!MASS -1 Co2p 58.93300 ! Cobalt -!MASS -1 Ni2p 58.69300 ! Nickel -!MASS -1 Cu2p 63.54600 ! Copper +MASS -1 Ra2p 226.03000 ! Radium +MASS -1 V2p 50.94200 ! Vanadium +MASS -1 Cr2p 51.99600 ! Chromium +MASS -1 Mn2p 54.93800 ! Manganese +MASS -1 Fe2p 55.85400 ! Iron +MASS -1 Co2p 58.93300 ! Cobalt +MASS -1 Ni2p 58.69300 ! Nickel +MASS -1 Cu2p 63.54600 ! Copper !MASS -1 Zn2p 65.38000 ! Zinc -!MASS -1 Pd2p 106.42000 ! Palladium -!MASS -1 Ag2p 107.87000 ! Silver +MASS -1 Pd2p 106.42000 ! Palladium +MASS -1 Ag2p 107.87000 ! Silver !MASS -1 Cd2p 1 12.41000 ! Cadmium -!MASS -1 Sn2p 118.71000 ! Tin -!MASS -1 Pt2p 195.08000 ! Platinum -!MASS -1 Hg2p 200.59000 ! Mercury -!MASS -1 Pb2p 207.20000 ! Lead -!MASS -1 Sm2p 150.36000 ! Samarium -!MASS -1 Eu2p 151.96000 ! Europium -!MASS -1 Yb2p 173.05000 ! Ytterbium -!MASS -1 Al3p 26.98200 ! Aluminum -!MASS -1 Sc3p 44.95600 ! Scandium -!MASS -1 Y3p 88.90600 ! Yttrium -!MASS -1 La3p 138.91000 ! Lanthanum -!MASS -1 Ce3p 140.12000 ! Cerium -!MASS -1 Pr3p 140.91000 ! Praseodynium -!MASS -1 Nd3p 144.24000 ! Neodynium -!MASS -1 Pm3p 144.91000 ! Promethium -!MASS -1 Sm3p 150.36000 ! Samarium -!MASS -1 Eu3p 151.96000 ! Europium -!MASS -1 Gd3p 157.25000 ! Gadolinium -!MASS -1 Tb3p 158.93000 ! Terbium -!MASS -1 Dy3p 162.50000 ! Dysprosium -!MASS -1 Ho3p 164.93000 ! Holmium -!MASS -1 Er3p 167.28000 ! Erbium -!MASS -1 Tm3p 168.93000 ! Thulium -!MASS -1 Yb3p 173.05000 ! Ytterbium -!MASS -1 Lu3p 174.97000 ! Lutetium -!MASS -1 U3p 238.03000 ! Uranium -!MASS -1 Pu3p 244.06000 ! Plutonium -!MASS -1 Ti3p 47.86700 ! Titanium -!MASS -1 V3p 50.94200 ! Vanadium -!MASS -1 Cr3p 51.99600 ! Chromium -!MASS -1 Mn3p 54.93800 ! Manganese -!MASS -1 Fe3p 55.85400 ! Iron -!MASS -1 Co3p 58.93300 ! Cobalt -!MASS -1 Ga3p 69.72300 ! Gallium -!MASS -1 Rh3p 102.91000 ! Rhodium -!MASS -1 In3p 114.82000 ! Indium -!MASS -1 Au3p 196.97000 ! Gold -!MASS -1 Tl3p 204.38000 ! Thallium -!MASS -1 Bi3p 208.98000 ! Bismuth -! +MASS -1 Sn2p 118.71000 ! Tin +MASS -1 Pt2p 195.08000 ! Platinum +MASS -1 Hg2p 200.59000 ! Mercury +MASS -1 Pb2p 207.20000 ! Lead +MASS -1 Sm2p 150.36000 ! Samarium +MASS -1 Eu2p 151.96000 ! Europium +MASS -1 Yb2p 173.05000 ! Ytterbium +MASS -1 Al3p 26.98200 ! Aluminum +MASS -1 Sc3p 44.95600 ! Scandium +MASS -1 Y3p 88.90600 ! Yttrium +MASS -1 La3p 138.91000 ! Lanthanum +MASS -1 Ce3p 140.12000 ! Cerium +MASS -1 Pr3p 140.91000 ! Praseodynium +MASS -1 Nd3p 144.24000 ! Neodynium +MASS -1 Pm3p 144.91000 ! Promethium +MASS -1 Sm3p 150.36000 ! Samarium +MASS -1 Eu3p 151.96000 ! Europium +MASS -1 Gd3p 157.25000 ! Gadolinium +MASS -1 Tb3p 158.93000 ! Terbium +MASS -1 Dy3p 162.50000 ! Dysprosium +MASS -1 Ho3p 164.93000 ! Holmium +MASS -1 Er3p 167.28000 ! Erbium +MASS -1 Tm3p 168.93000 ! Thulium +MASS -1 Yb3p 173.05000 ! Ytterbium +MASS -1 Lu3p 174.97000 ! Lutetium +MASS -1 U3p 238.03000 ! Uranium +MASS -1 Pu3p 244.06000 ! Plutonium +MASS -1 Ti3p 47.86700 ! Titanium +MASS -1 V3p 50.94200 ! Vanadium +MASS -1 Cr3p 51.99600 ! Chromium +MASS -1 Mn3p 54.93800 ! Manganese +MASS -1 Fe3p 55.85400 ! Iron +MASS -1 Co3p 58.93300 ! Cobalt +MASS -1 Ga3p 69.72300 ! Gallium +MASS -1 Rh3p 102.91000 ! Rhodium +MASS -1 In3p 114.82000 ! Indium +MASS -1 Au3p 196.97000 ! Gold +MASS -1 Tl3p 204.38000 ! Thallium +MASS -1 Bi3p 208.98000 ! Bismuth + !standard C36 additive truncation BONDS !Following lines added from par_all36m_prot.prm @@ -3568,7 +3568,7 @@ C NH1 CT2 C NH1 CT2 C N 24 NONBONDED !Following lines added from par_all36m_prot.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 2013 correction ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] @@ -3685,7 +3685,7 @@ SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 !Following lines added from par_water_ions.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !TIP3P LJ parameters HT 0.0 -0.046 0.2245 @@ -3726,7 +3726,7 @@ CLA 0.0 -0.150 2.27 ! Chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol !Following lines added from par_all36_prot_arg0.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme !methylguanidine parameters HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 @@ -3742,9 +3742,8 @@ NRN1 0.0 -0.4500 2.0000 ! aliphatic amines NRN2 0.0 -0.0600 1.9900 ! aliphatic amines !end methylguanidine -!END !Following lines added from par_ions_won.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !truncation scheme used in JPCA 2012 paper under stochastic !boundary conditions. @@ -3820,7 +3819,6 @@ Au3p 0.0 -0.1330 0.3654 ! dA = -4420 kJ/mol Tl3p 0.0 -0.1629 0.8693 ! dA = -3970 kJ/mol Bi3p 0.0 -0.1850 1.3682 ! dA = -3480 kJ/mol -!END NBFIX !Following lines added from par_all36m_prot.prm ! Emin Rmin @@ -3832,7 +3830,6 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! (kcal/mol) (A) !SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 !POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189, repeated below -!END ! The following section contains NBFixes for sodium interacting with ! carboxylate oxygens of various CHARMM force fields. It will generate @@ -3845,12 +3842,12 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! want the NBFixes to apply. A more elegant solution would require new ! features to be added to CHARMM. ! parallel fix, to avoid duplicated messages in the log -!set para -!if ?NUMNODE gt 1 set para node 0 +set para +if ?NUMNODE gt 1 set para node 0 -!set wrn ?WRNLEV +set wrn ?WRNLEV ! Some versions of CHARMM don't seem to initialize wrnlev... -!if "@WRN" eq "?WRNLEV" set wrn 5 +if "@WRN" eq "?WRNLEV" set wrn 5 HBOND !Following lines added from par_all36m_prot.prm ! READ PARAM APPEND CARD diff --git a/test-charmm-build/1GZM/parameters b/test-charmm-build/1GZM/parameters index f667868..6dc1448 100644 --- a/test-charmm-build/1GZM/parameters +++ b/test-charmm-build/1GZM/parameters @@ -5,7 +5,7 @@ * All comments to the CHARMM web site: www.charmm.org * parameter set discussion forum * -! + !references ! !Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M, de Groot, B.L., @@ -32,169 +32,169 @@ !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. -! + * Parameters for water and ions * -! -! + + * par_cation.prm for mono-, di-, and trivalent cations * -! -!ATOMS + +ATOMS !Following lines added from par_all36m_prot.prm -!MASS -1 H 1.00800 ! polar H -!MASS -1 HC 1.00800 ! N-ter H -!MASS -1 HA 1.00800 ! nonpolar H -!MASS -1 HP 1.00800 ! aromatic H -!MASS -1 HB1 1.00800 ! backbone H -!MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 -!MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 -!MASS -1 HR2 1.00800 ! (+) his HE1 -!MASS -1 HR3 1.00800 ! neutral his HG, HD2 -!MASS -1 HS 1.00800 ! thiol hydrogen -!MASS -1 HE1 1.00800 ! for alkene; RHC=CR -!MASS -1 HE2 1.00800 ! for alkene; H2C=CR -!MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 C 12.01100 ! carbonyl C, peptide backbone -!MASS -1 CA 12.01100 ! aromatic C -!MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters -!MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH -!MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 -!MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu -!MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 -!MASS -1 CPH1 12.01100 ! his CG and CD2 carbons -!MASS -1 CPH2 12.01100 ! his CE1 carbon -!MASS -1 CPT 12.01100 ! trp C between rings -!MASS -1 CY 12.01100 ! TRP C in pyrrole ring -!MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) -!MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) -!MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) -!MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 -!MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 -!MASS -1 CS 12.01100 ! thiolate carbon -!MASS -1 CE1 12.01100 ! for alkene; RHC=CR -!MASS -1 CE2 12.01100 ! for alkene; H2C=CR -!MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp -!MASS -1 C3 12.01100 ! cyclopropane carbon -!MASS -1 N 14.00700 ! proline N -!MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen -!MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen -!MASS -1 NR3 14.00700 ! charged his ring nitrogen -!MASS -1 NH1 14.00700 ! peptide nitrogen -!MASS -1 NH2 14.00700 ! amide nitrogen -!MASS -1 NH3 14.00700 ! ammonium nitrogen -!MASS -1 NC2 14.00700 ! guanidinium nitrogen -!MASS -1 NY 14.00700 ! TRP N in pyrrole ring -!MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) -!MASS -1 O 15.99900 ! carbonyl oxygen -!MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid -!MASS -1 OC 15.99900 ! carboxylate oxygen -!MASS -1 OH1 15.99900 ! hydroxyl oxygen -!MASS -1 OS 15.99940 ! ester oxygen -!MASS -1 S 32.06000 ! sulphur -!MASS -1 SM 32.06000 ! sulfur C-S-S-C type -!MASS -1 SS 32.06000 ! thiolate sulfur -! -! +MASS -1 H 1.00800 ! polar H +MASS -1 HC 1.00800 ! N-ter H +MASS -1 HA 1.00800 ! nonpolar H +MASS -1 HP 1.00800 ! aromatic H +MASS -1 HB1 1.00800 ! backbone H +MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS -1 HR2 1.00800 ! (+) his HE1 +MASS -1 HR3 1.00800 ! neutral his HG, HD2 +MASS -1 HS 1.00800 ! thiol hydrogen +MASS -1 HE1 1.00800 ! for alkene; RHC=CR +MASS -1 HE2 1.00800 ! for alkene; H2C=CR +MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 C 12.01100 ! carbonyl C, peptide backbone +MASS -1 CA 12.01100 ! aromatic C +MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters +MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH +MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu +MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS -1 CPH1 12.01100 ! his CG and CD2 carbons +MASS -1 CPH2 12.01100 ! his CE1 carbon +MASS -1 CPT 12.01100 ! trp C between rings +MASS -1 CY 12.01100 ! TRP C in pyrrole ring +MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) +MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) +MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS -1 CS 12.01100 ! thiolate carbon +MASS -1 CE1 12.01100 ! for alkene; RHC=CR +MASS -1 CE2 12.01100 ! for alkene; H2C=CR +MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp +MASS -1 C3 12.01100 ! cyclopropane carbon +MASS -1 N 14.00700 ! proline N +MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS -1 NR3 14.00700 ! charged his ring nitrogen +MASS -1 NH1 14.00700 ! peptide nitrogen +MASS -1 NH2 14.00700 ! amide nitrogen +MASS -1 NH3 14.00700 ! ammonium nitrogen +MASS -1 NC2 14.00700 ! guanidinium nitrogen +MASS -1 NY 14.00700 ! TRP N in pyrrole ring +MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS -1 O 15.99900 ! carbonyl oxygen +MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS -1 OC 15.99900 ! carboxylate oxygen +MASS -1 OH1 15.99900 ! hydroxyl oxygen +MASS -1 OS 15.99940 ! ester oxygen +MASS -1 S 32.06000 ! sulphur +MASS -1 SM 32.06000 ! sulfur C-S-S-C type +MASS -1 SS 32.06000 ! thiolate sulfur + + !Following lines added from par_water_ions.prm -!MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN -!MASS -1 HX 1.00800 ! hydroxide hydrogen -!MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN -!MASS -1 OX 15.99940 ! hydroxide oxygen -!MASS -1 HPER 1.00800 ! H of H2O2 -!MASS -1 OPER 15.99900 ! O of H2O2 -!MASS -1 LIT 6.94100 ! Lithium ion -!MASS -1 SOD 22.98977 ! Sodium Ion -!MASS -1 MG 24.30500 ! Magnesium Ion -!MASS -1 POT 39.09830 ! Potassium Ion -!MASS -1 CAL 40.08000 ! Calcium Ion -!MASS -1 RUB 85.46780 ! Rubidium Ion -!MASS -1 CES 132.90545 ! Cesium Ion -!MASS -1 BAR 137.32700 ! Barium Ion -!MASS -1 ZN 65.37000 ! zinc (II) cation -!MASS -1 CAD 112.41100 ! cadmium (II) cation -!MASS -1 CLA 35.45000 ! Chloride Ion -! +MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS -1 HX 1.00800 ! hydroxide hydrogen +MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS -1 OX 15.99940 ! hydroxide oxygen +MASS -1 HPER 1.00800 ! H of H2O2 +MASS -1 OPER 15.99900 ! O of H2O2 +MASS -1 LIT 6.94100 ! Lithium ion +MASS -1 SOD 22.98977 ! Sodium Ion +MASS -1 MG 24.30500 ! Magnesium Ion +MASS -1 POT 39.09830 ! Potassium Ion +MASS -1 CAL 40.08000 ! Calcium Ion +MASS -1 RUB 85.46780 ! Rubidium Ion +MASS -1 CES 132.90545 ! Cesium Ion +MASS -1 BAR 137.32700 ! Barium Ion +MASS -1 ZN 65.37000 ! zinc (II) cation +MASS -1 CAD 112.41100 ! cadmium (II) cation +MASS -1 CLA 35.45000 ! Chloride Ion + !Following lines added from par_all36_prot_arg0.prm -!MASS -1 HRA3 1.00800 ! alphatic proton, CH3 -!MASS -1 HRP2 1.00800 ! polar H, +ve charge -!MASS -1 HRM1 1.00800 ! polar H, dimethylamine -!MASS -1 HRM2 1.00800 ! polar H, methylamine -!MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium -!MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) -!MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base -!MASS -1 NRN1 14.00700 ! dimethylamine nitrogen -!MASS -1 NRN2 14.00700 ! methylamine nitrogen -! +MASS -1 HRA3 1.00800 ! alphatic proton, CH3 +MASS -1 HRP2 1.00800 ! polar H, +ve charge +MASS -1 HRM1 1.00800 ! polar H, dimethylamine +MASS -1 HRM2 1.00800 ! polar H, methylamine +MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium +MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) +MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base +MASS -1 NRN1 14.00700 ! dimethylamine nitrogen +MASS -1 NRN2 14.00700 ! methylamine nitrogen + !Following lines added from par_ions_won.prm !MASS -1 Li1p 6.94000 ! Lithium !MASS -1 Na1p 22.99000 ! Sodium !MASS -1 K1p 39.09000 ! Potassium !MASS -1 Rb1p 85.46000 ! Rubidium !MASS -1 Cs1p 132.91000 ! Cesium -!MASS -1 Cu1p 63.54600 ! Copper -!MASS -1 Ag1p 107.87000 ! Silver -!MASS -1 Au1p 196.97000 ! Gold -!MASS -1 Ti1p 47.86700 ! Titanium -!MASS -1 Be2p 9.01220 ! Beryllium +MASS -1 Cu1p 63.54600 ! Copper +MASS -1 Ag1p 107.87000 ! Silver +MASS -1 Au1p 196.97000 ! Gold +MASS -1 Ti1p 47.86700 ! Titanium +MASS -1 Be2p 9.01220 ! Beryllium !MASS -1 Mg2p 24.30500 ! Magnesium !MASS -1 Ca2p 40.07800 ! Calcium -!MASS -1 Sr2p 87.62000 ! Strontium +MASS -1 Sr2p 87.62000 ! Strontium !MASS -1 Ba2p 1 37.33 00 ! Barium -!MASS -1 Ra2p 226.03000 ! Radium -!MASS -1 V2p 50.94200 ! Vanadium -!MASS -1 Cr2p 51.99600 ! Chromium -!MASS -1 Mn2p 54.93800 ! Manganese -!MASS -1 Fe2p 55.85400 ! Iron -!MASS -1 Co2p 58.93300 ! Cobalt -!MASS -1 Ni2p 58.69300 ! Nickel -!MASS -1 Cu2p 63.54600 ! Copper +MASS -1 Ra2p 226.03000 ! Radium +MASS -1 V2p 50.94200 ! Vanadium +MASS -1 Cr2p 51.99600 ! Chromium +MASS -1 Mn2p 54.93800 ! Manganese +MASS -1 Fe2p 55.85400 ! Iron +MASS -1 Co2p 58.93300 ! Cobalt +MASS -1 Ni2p 58.69300 ! Nickel +MASS -1 Cu2p 63.54600 ! Copper !MASS -1 Zn2p 65.38000 ! Zinc -!MASS -1 Pd2p 106.42000 ! Palladium -!MASS -1 Ag2p 107.87000 ! Silver +MASS -1 Pd2p 106.42000 ! Palladium +MASS -1 Ag2p 107.87000 ! Silver !MASS -1 Cd2p 1 12.41000 ! Cadmium -!MASS -1 Sn2p 118.71000 ! Tin -!MASS -1 Pt2p 195.08000 ! Platinum -!MASS -1 Hg2p 200.59000 ! Mercury -!MASS -1 Pb2p 207.20000 ! Lead -!MASS -1 Sm2p 150.36000 ! Samarium -!MASS -1 Eu2p 151.96000 ! Europium -!MASS -1 Yb2p 173.05000 ! Ytterbium -!MASS -1 Al3p 26.98200 ! Aluminum -!MASS -1 Sc3p 44.95600 ! Scandium -!MASS -1 Y3p 88.90600 ! Yttrium -!MASS -1 La3p 138.91000 ! Lanthanum -!MASS -1 Ce3p 140.12000 ! Cerium -!MASS -1 Pr3p 140.91000 ! Praseodynium -!MASS -1 Nd3p 144.24000 ! Neodynium -!MASS -1 Pm3p 144.91000 ! Promethium -!MASS -1 Sm3p 150.36000 ! Samarium -!MASS -1 Eu3p 151.96000 ! Europium -!MASS -1 Gd3p 157.25000 ! Gadolinium -!MASS -1 Tb3p 158.93000 ! Terbium -!MASS -1 Dy3p 162.50000 ! Dysprosium -!MASS -1 Ho3p 164.93000 ! Holmium -!MASS -1 Er3p 167.28000 ! Erbium -!MASS -1 Tm3p 168.93000 ! Thulium -!MASS -1 Yb3p 173.05000 ! Ytterbium -!MASS -1 Lu3p 174.97000 ! Lutetium -!MASS -1 U3p 238.03000 ! Uranium -!MASS -1 Pu3p 244.06000 ! Plutonium -!MASS -1 Ti3p 47.86700 ! Titanium -!MASS -1 V3p 50.94200 ! Vanadium -!MASS -1 Cr3p 51.99600 ! Chromium -!MASS -1 Mn3p 54.93800 ! Manganese -!MASS -1 Fe3p 55.85400 ! Iron -!MASS -1 Co3p 58.93300 ! Cobalt -!MASS -1 Ga3p 69.72300 ! Gallium -!MASS -1 Rh3p 102.91000 ! Rhodium -!MASS -1 In3p 114.82000 ! Indium -!MASS -1 Au3p 196.97000 ! Gold -!MASS -1 Tl3p 204.38000 ! Thallium -!MASS -1 Bi3p 208.98000 ! Bismuth -! +MASS -1 Sn2p 118.71000 ! Tin +MASS -1 Pt2p 195.08000 ! Platinum +MASS -1 Hg2p 200.59000 ! Mercury +MASS -1 Pb2p 207.20000 ! Lead +MASS -1 Sm2p 150.36000 ! Samarium +MASS -1 Eu2p 151.96000 ! Europium +MASS -1 Yb2p 173.05000 ! Ytterbium +MASS -1 Al3p 26.98200 ! Aluminum +MASS -1 Sc3p 44.95600 ! Scandium +MASS -1 Y3p 88.90600 ! Yttrium +MASS -1 La3p 138.91000 ! Lanthanum +MASS -1 Ce3p 140.12000 ! Cerium +MASS -1 Pr3p 140.91000 ! Praseodynium +MASS -1 Nd3p 144.24000 ! Neodynium +MASS -1 Pm3p 144.91000 ! Promethium +MASS -1 Sm3p 150.36000 ! Samarium +MASS -1 Eu3p 151.96000 ! Europium +MASS -1 Gd3p 157.25000 ! Gadolinium +MASS -1 Tb3p 158.93000 ! Terbium +MASS -1 Dy3p 162.50000 ! Dysprosium +MASS -1 Ho3p 164.93000 ! Holmium +MASS -1 Er3p 167.28000 ! Erbium +MASS -1 Tm3p 168.93000 ! Thulium +MASS -1 Yb3p 173.05000 ! Ytterbium +MASS -1 Lu3p 174.97000 ! Lutetium +MASS -1 U3p 238.03000 ! Uranium +MASS -1 Pu3p 244.06000 ! Plutonium +MASS -1 Ti3p 47.86700 ! Titanium +MASS -1 V3p 50.94200 ! Vanadium +MASS -1 Cr3p 51.99600 ! Chromium +MASS -1 Mn3p 54.93800 ! Manganese +MASS -1 Fe3p 55.85400 ! Iron +MASS -1 Co3p 58.93300 ! Cobalt +MASS -1 Ga3p 69.72300 ! Gallium +MASS -1 Rh3p 102.91000 ! Rhodium +MASS -1 In3p 114.82000 ! Indium +MASS -1 Au3p 196.97000 ! Gold +MASS -1 Tl3p 204.38000 ! Thallium +MASS -1 Bi3p 208.98000 ! Bismuth + !standard C36 additive truncation BONDS !Following lines added from par_all36m_prot.prm @@ -3568,7 +3568,7 @@ C NH1 CT2 C NH1 CT2 C N 24 NONBONDED !Following lines added from par_all36m_prot.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 2013 correction ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] @@ -3685,7 +3685,7 @@ SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 !Following lines added from par_water_ions.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !TIP3P LJ parameters HT 0.0 -0.046 0.2245 @@ -3726,7 +3726,7 @@ CLA 0.0 -0.150 2.27 ! Chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol !Following lines added from par_all36_prot_arg0.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme !methylguanidine parameters HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 @@ -3742,9 +3742,8 @@ NRN1 0.0 -0.4500 2.0000 ! aliphatic amines NRN2 0.0 -0.0600 1.9900 ! aliphatic amines !end methylguanidine -!END !Following lines added from par_ions_won.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !truncation scheme used in JPCA 2012 paper under stochastic !boundary conditions. @@ -3820,7 +3819,6 @@ Au3p 0.0 -0.1330 0.3654 ! dA = -4420 kJ/mol Tl3p 0.0 -0.1629 0.8693 ! dA = -3970 kJ/mol Bi3p 0.0 -0.1850 1.3682 ! dA = -3480 kJ/mol -!END NBFIX !Following lines added from par_all36m_prot.prm ! Emin Rmin @@ -3832,7 +3830,6 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! (kcal/mol) (A) !SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 !POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189, repeated below -!END ! The following section contains NBFixes for sodium interacting with ! carboxylate oxygens of various CHARMM force fields. It will generate @@ -3845,12 +3842,12 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! want the NBFixes to apply. A more elegant solution would require new ! features to be added to CHARMM. ! parallel fix, to avoid duplicated messages in the log -!set para -!if ?NUMNODE gt 1 set para node 0 +set para +if ?NUMNODE gt 1 set para node 0 -!set wrn ?WRNLEV +set wrn ?WRNLEV ! Some versions of CHARMM don't seem to initialize wrnlev... -!if "@WRN" eq "?WRNLEV" set wrn 5 +if "@WRN" eq "?WRNLEV" set wrn 5 HBOND !Following lines added from par_all36m_prot.prm ! READ PARAM APPEND CARD diff --git a/test-charmm-build/1U5U/parameters b/test-charmm-build/1U5U/parameters index f667868..6dc1448 100644 --- a/test-charmm-build/1U5U/parameters +++ b/test-charmm-build/1U5U/parameters @@ -5,7 +5,7 @@ * All comments to the CHARMM web site: www.charmm.org * parameter set discussion forum * -! + !references ! !Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M, de Groot, B.L., @@ -32,169 +32,169 @@ !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. -! + * Parameters for water and ions * -! -! + + * par_cation.prm for mono-, di-, and trivalent cations * -! -!ATOMS + +ATOMS !Following lines added from par_all36m_prot.prm -!MASS -1 H 1.00800 ! polar H -!MASS -1 HC 1.00800 ! N-ter H -!MASS -1 HA 1.00800 ! nonpolar H -!MASS -1 HP 1.00800 ! aromatic H -!MASS -1 HB1 1.00800 ! backbone H -!MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 -!MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 -!MASS -1 HR2 1.00800 ! (+) his HE1 -!MASS -1 HR3 1.00800 ! neutral his HG, HD2 -!MASS -1 HS 1.00800 ! thiol hydrogen -!MASS -1 HE1 1.00800 ! for alkene; RHC=CR -!MASS -1 HE2 1.00800 ! for alkene; H2C=CR -!MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 C 12.01100 ! carbonyl C, peptide backbone -!MASS -1 CA 12.01100 ! aromatic C -!MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters -!MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH -!MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 -!MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu -!MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 -!MASS -1 CPH1 12.01100 ! his CG and CD2 carbons -!MASS -1 CPH2 12.01100 ! his CE1 carbon -!MASS -1 CPT 12.01100 ! trp C between rings -!MASS -1 CY 12.01100 ! TRP C in pyrrole ring -!MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) -!MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) -!MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) -!MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 -!MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 -!MASS -1 CS 12.01100 ! thiolate carbon -!MASS -1 CE1 12.01100 ! for alkene; RHC=CR -!MASS -1 CE2 12.01100 ! for alkene; H2C=CR -!MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp -!MASS -1 C3 12.01100 ! cyclopropane carbon -!MASS -1 N 14.00700 ! proline N -!MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen -!MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen -!MASS -1 NR3 14.00700 ! charged his ring nitrogen -!MASS -1 NH1 14.00700 ! peptide nitrogen -!MASS -1 NH2 14.00700 ! amide nitrogen -!MASS -1 NH3 14.00700 ! ammonium nitrogen -!MASS -1 NC2 14.00700 ! guanidinium nitrogen -!MASS -1 NY 14.00700 ! TRP N in pyrrole ring -!MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) -!MASS -1 O 15.99900 ! carbonyl oxygen -!MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid -!MASS -1 OC 15.99900 ! carboxylate oxygen -!MASS -1 OH1 15.99900 ! hydroxyl oxygen -!MASS -1 OS 15.99940 ! ester oxygen -!MASS -1 S 32.06000 ! sulphur -!MASS -1 SM 32.06000 ! sulfur C-S-S-C type -!MASS -1 SS 32.06000 ! thiolate sulfur -! -! +MASS -1 H 1.00800 ! polar H +MASS -1 HC 1.00800 ! N-ter H +MASS -1 HA 1.00800 ! nonpolar H +MASS -1 HP 1.00800 ! aromatic H +MASS -1 HB1 1.00800 ! backbone H +MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS -1 HR2 1.00800 ! (+) his HE1 +MASS -1 HR3 1.00800 ! neutral his HG, HD2 +MASS -1 HS 1.00800 ! thiol hydrogen +MASS -1 HE1 1.00800 ! for alkene; RHC=CR +MASS -1 HE2 1.00800 ! for alkene; H2C=CR +MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 C 12.01100 ! carbonyl C, peptide backbone +MASS -1 CA 12.01100 ! aromatic C +MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters +MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH +MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu +MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS -1 CPH1 12.01100 ! his CG and CD2 carbons +MASS -1 CPH2 12.01100 ! his CE1 carbon +MASS -1 CPT 12.01100 ! trp C between rings +MASS -1 CY 12.01100 ! TRP C in pyrrole ring +MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) +MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) +MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS -1 CS 12.01100 ! thiolate carbon +MASS -1 CE1 12.01100 ! for alkene; RHC=CR +MASS -1 CE2 12.01100 ! for alkene; H2C=CR +MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp +MASS -1 C3 12.01100 ! cyclopropane carbon +MASS -1 N 14.00700 ! proline N +MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS -1 NR3 14.00700 ! charged his ring nitrogen +MASS -1 NH1 14.00700 ! peptide nitrogen +MASS -1 NH2 14.00700 ! amide nitrogen +MASS -1 NH3 14.00700 ! ammonium nitrogen +MASS -1 NC2 14.00700 ! guanidinium nitrogen +MASS -1 NY 14.00700 ! TRP N in pyrrole ring +MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS -1 O 15.99900 ! carbonyl oxygen +MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS -1 OC 15.99900 ! carboxylate oxygen +MASS -1 OH1 15.99900 ! hydroxyl oxygen +MASS -1 OS 15.99940 ! ester oxygen +MASS -1 S 32.06000 ! sulphur +MASS -1 SM 32.06000 ! sulfur C-S-S-C type +MASS -1 SS 32.06000 ! thiolate sulfur + + !Following lines added from par_water_ions.prm -!MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN -!MASS -1 HX 1.00800 ! hydroxide hydrogen -!MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN -!MASS -1 OX 15.99940 ! hydroxide oxygen -!MASS -1 HPER 1.00800 ! H of H2O2 -!MASS -1 OPER 15.99900 ! O of H2O2 -!MASS -1 LIT 6.94100 ! Lithium ion -!MASS -1 SOD 22.98977 ! Sodium Ion -!MASS -1 MG 24.30500 ! Magnesium Ion -!MASS -1 POT 39.09830 ! Potassium Ion -!MASS -1 CAL 40.08000 ! Calcium Ion -!MASS -1 RUB 85.46780 ! Rubidium Ion -!MASS -1 CES 132.90545 ! Cesium Ion -!MASS -1 BAR 137.32700 ! Barium Ion -!MASS -1 ZN 65.37000 ! zinc (II) cation -!MASS -1 CAD 112.41100 ! cadmium (II) cation -!MASS -1 CLA 35.45000 ! Chloride Ion -! +MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS -1 HX 1.00800 ! hydroxide hydrogen +MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS -1 OX 15.99940 ! hydroxide oxygen +MASS -1 HPER 1.00800 ! H of H2O2 +MASS -1 OPER 15.99900 ! O of H2O2 +MASS -1 LIT 6.94100 ! Lithium ion +MASS -1 SOD 22.98977 ! Sodium Ion +MASS -1 MG 24.30500 ! Magnesium Ion +MASS -1 POT 39.09830 ! Potassium Ion +MASS -1 CAL 40.08000 ! Calcium Ion +MASS -1 RUB 85.46780 ! Rubidium Ion +MASS -1 CES 132.90545 ! Cesium Ion +MASS -1 BAR 137.32700 ! Barium Ion +MASS -1 ZN 65.37000 ! zinc (II) cation +MASS -1 CAD 112.41100 ! cadmium (II) cation +MASS -1 CLA 35.45000 ! Chloride Ion + !Following lines added from par_all36_prot_arg0.prm -!MASS -1 HRA3 1.00800 ! alphatic proton, CH3 -!MASS -1 HRP2 1.00800 ! polar H, +ve charge -!MASS -1 HRM1 1.00800 ! polar H, dimethylamine -!MASS -1 HRM2 1.00800 ! polar H, methylamine -!MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium -!MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) -!MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base -!MASS -1 NRN1 14.00700 ! dimethylamine nitrogen -!MASS -1 NRN2 14.00700 ! methylamine nitrogen -! +MASS -1 HRA3 1.00800 ! alphatic proton, CH3 +MASS -1 HRP2 1.00800 ! polar H, +ve charge +MASS -1 HRM1 1.00800 ! polar H, dimethylamine +MASS -1 HRM2 1.00800 ! polar H, methylamine +MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium +MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) +MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base +MASS -1 NRN1 14.00700 ! dimethylamine nitrogen +MASS -1 NRN2 14.00700 ! methylamine nitrogen + !Following lines added from par_ions_won.prm !MASS -1 Li1p 6.94000 ! Lithium !MASS -1 Na1p 22.99000 ! Sodium !MASS -1 K1p 39.09000 ! Potassium !MASS -1 Rb1p 85.46000 ! Rubidium !MASS -1 Cs1p 132.91000 ! Cesium -!MASS -1 Cu1p 63.54600 ! Copper -!MASS -1 Ag1p 107.87000 ! Silver -!MASS -1 Au1p 196.97000 ! Gold -!MASS -1 Ti1p 47.86700 ! Titanium -!MASS -1 Be2p 9.01220 ! Beryllium +MASS -1 Cu1p 63.54600 ! Copper +MASS -1 Ag1p 107.87000 ! Silver +MASS -1 Au1p 196.97000 ! Gold +MASS -1 Ti1p 47.86700 ! Titanium +MASS -1 Be2p 9.01220 ! Beryllium !MASS -1 Mg2p 24.30500 ! Magnesium !MASS -1 Ca2p 40.07800 ! Calcium -!MASS -1 Sr2p 87.62000 ! Strontium +MASS -1 Sr2p 87.62000 ! Strontium !MASS -1 Ba2p 1 37.33 00 ! Barium -!MASS -1 Ra2p 226.03000 ! Radium -!MASS -1 V2p 50.94200 ! Vanadium -!MASS -1 Cr2p 51.99600 ! Chromium -!MASS -1 Mn2p 54.93800 ! Manganese -!MASS -1 Fe2p 55.85400 ! Iron -!MASS -1 Co2p 58.93300 ! Cobalt -!MASS -1 Ni2p 58.69300 ! Nickel -!MASS -1 Cu2p 63.54600 ! Copper +MASS -1 Ra2p 226.03000 ! Radium +MASS -1 V2p 50.94200 ! Vanadium +MASS -1 Cr2p 51.99600 ! Chromium +MASS -1 Mn2p 54.93800 ! Manganese +MASS -1 Fe2p 55.85400 ! Iron +MASS -1 Co2p 58.93300 ! Cobalt +MASS -1 Ni2p 58.69300 ! Nickel +MASS -1 Cu2p 63.54600 ! Copper !MASS -1 Zn2p 65.38000 ! Zinc -!MASS -1 Pd2p 106.42000 ! Palladium -!MASS -1 Ag2p 107.87000 ! Silver +MASS -1 Pd2p 106.42000 ! Palladium +MASS -1 Ag2p 107.87000 ! Silver !MASS -1 Cd2p 1 12.41000 ! Cadmium -!MASS -1 Sn2p 118.71000 ! Tin -!MASS -1 Pt2p 195.08000 ! Platinum -!MASS -1 Hg2p 200.59000 ! Mercury -!MASS -1 Pb2p 207.20000 ! Lead -!MASS -1 Sm2p 150.36000 ! Samarium -!MASS -1 Eu2p 151.96000 ! Europium -!MASS -1 Yb2p 173.05000 ! Ytterbium -!MASS -1 Al3p 26.98200 ! Aluminum -!MASS -1 Sc3p 44.95600 ! Scandium -!MASS -1 Y3p 88.90600 ! Yttrium -!MASS -1 La3p 138.91000 ! Lanthanum -!MASS -1 Ce3p 140.12000 ! Cerium -!MASS -1 Pr3p 140.91000 ! Praseodynium -!MASS -1 Nd3p 144.24000 ! Neodynium -!MASS -1 Pm3p 144.91000 ! Promethium -!MASS -1 Sm3p 150.36000 ! Samarium -!MASS -1 Eu3p 151.96000 ! Europium -!MASS -1 Gd3p 157.25000 ! Gadolinium -!MASS -1 Tb3p 158.93000 ! Terbium -!MASS -1 Dy3p 162.50000 ! Dysprosium -!MASS -1 Ho3p 164.93000 ! Holmium -!MASS -1 Er3p 167.28000 ! Erbium -!MASS -1 Tm3p 168.93000 ! Thulium -!MASS -1 Yb3p 173.05000 ! Ytterbium -!MASS -1 Lu3p 174.97000 ! Lutetium -!MASS -1 U3p 238.03000 ! Uranium -!MASS -1 Pu3p 244.06000 ! Plutonium -!MASS -1 Ti3p 47.86700 ! Titanium -!MASS -1 V3p 50.94200 ! Vanadium -!MASS -1 Cr3p 51.99600 ! Chromium -!MASS -1 Mn3p 54.93800 ! Manganese -!MASS -1 Fe3p 55.85400 ! Iron -!MASS -1 Co3p 58.93300 ! Cobalt -!MASS -1 Ga3p 69.72300 ! Gallium -!MASS -1 Rh3p 102.91000 ! Rhodium -!MASS -1 In3p 114.82000 ! Indium -!MASS -1 Au3p 196.97000 ! Gold -!MASS -1 Tl3p 204.38000 ! Thallium -!MASS -1 Bi3p 208.98000 ! Bismuth -! +MASS -1 Sn2p 118.71000 ! Tin +MASS -1 Pt2p 195.08000 ! Platinum +MASS -1 Hg2p 200.59000 ! Mercury +MASS -1 Pb2p 207.20000 ! Lead +MASS -1 Sm2p 150.36000 ! Samarium +MASS -1 Eu2p 151.96000 ! Europium +MASS -1 Yb2p 173.05000 ! Ytterbium +MASS -1 Al3p 26.98200 ! Aluminum +MASS -1 Sc3p 44.95600 ! Scandium +MASS -1 Y3p 88.90600 ! Yttrium +MASS -1 La3p 138.91000 ! Lanthanum +MASS -1 Ce3p 140.12000 ! Cerium +MASS -1 Pr3p 140.91000 ! Praseodynium +MASS -1 Nd3p 144.24000 ! Neodynium +MASS -1 Pm3p 144.91000 ! Promethium +MASS -1 Sm3p 150.36000 ! Samarium +MASS -1 Eu3p 151.96000 ! Europium +MASS -1 Gd3p 157.25000 ! Gadolinium +MASS -1 Tb3p 158.93000 ! Terbium +MASS -1 Dy3p 162.50000 ! Dysprosium +MASS -1 Ho3p 164.93000 ! Holmium +MASS -1 Er3p 167.28000 ! Erbium +MASS -1 Tm3p 168.93000 ! Thulium +MASS -1 Yb3p 173.05000 ! Ytterbium +MASS -1 Lu3p 174.97000 ! Lutetium +MASS -1 U3p 238.03000 ! Uranium +MASS -1 Pu3p 244.06000 ! Plutonium +MASS -1 Ti3p 47.86700 ! Titanium +MASS -1 V3p 50.94200 ! Vanadium +MASS -1 Cr3p 51.99600 ! Chromium +MASS -1 Mn3p 54.93800 ! Manganese +MASS -1 Fe3p 55.85400 ! Iron +MASS -1 Co3p 58.93300 ! Cobalt +MASS -1 Ga3p 69.72300 ! Gallium +MASS -1 Rh3p 102.91000 ! Rhodium +MASS -1 In3p 114.82000 ! Indium +MASS -1 Au3p 196.97000 ! Gold +MASS -1 Tl3p 204.38000 ! Thallium +MASS -1 Bi3p 208.98000 ! Bismuth + !standard C36 additive truncation BONDS !Following lines added from par_all36m_prot.prm @@ -3568,7 +3568,7 @@ C NH1 CT2 C NH1 CT2 C N 24 NONBONDED !Following lines added from par_all36m_prot.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 2013 correction ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] @@ -3685,7 +3685,7 @@ SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 !Following lines added from par_water_ions.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !TIP3P LJ parameters HT 0.0 -0.046 0.2245 @@ -3726,7 +3726,7 @@ CLA 0.0 -0.150 2.27 ! Chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol !Following lines added from par_all36_prot_arg0.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme !methylguanidine parameters HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 @@ -3742,9 +3742,8 @@ NRN1 0.0 -0.4500 2.0000 ! aliphatic amines NRN2 0.0 -0.0600 1.9900 ! aliphatic amines !end methylguanidine -!END !Following lines added from par_ions_won.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !truncation scheme used in JPCA 2012 paper under stochastic !boundary conditions. @@ -3820,7 +3819,6 @@ Au3p 0.0 -0.1330 0.3654 ! dA = -4420 kJ/mol Tl3p 0.0 -0.1629 0.8693 ! dA = -3970 kJ/mol Bi3p 0.0 -0.1850 1.3682 ! dA = -3480 kJ/mol -!END NBFIX !Following lines added from par_all36m_prot.prm ! Emin Rmin @@ -3832,7 +3830,6 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! (kcal/mol) (A) !SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 !POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189, repeated below -!END ! The following section contains NBFixes for sodium interacting with ! carboxylate oxygens of various CHARMM force fields. It will generate @@ -3845,12 +3842,12 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! want the NBFixes to apply. A more elegant solution would require new ! features to be added to CHARMM. ! parallel fix, to avoid duplicated messages in the log -!set para -!if ?NUMNODE gt 1 set para node 0 +set para +if ?NUMNODE gt 1 set para node 0 -!set wrn ?WRNLEV +set wrn ?WRNLEV ! Some versions of CHARMM don't seem to initialize wrnlev... -!if "@WRN" eq "?WRNLEV" set wrn 5 +if "@WRN" eq "?WRNLEV" set wrn 5 HBOND !Following lines added from par_all36m_prot.prm ! READ PARAM APPEND CARD diff --git a/test-charmm-build/3PTB/parameters b/test-charmm-build/3PTB/parameters index f667868..6dc1448 100644 --- a/test-charmm-build/3PTB/parameters +++ b/test-charmm-build/3PTB/parameters @@ -5,7 +5,7 @@ * All comments to the CHARMM web site: www.charmm.org * parameter set discussion forum * -! + !references ! !Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M, de Groot, B.L., @@ -32,169 +32,169 @@ !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. -! + * Parameters for water and ions * -! -! + + * par_cation.prm for mono-, di-, and trivalent cations * -! -!ATOMS + +ATOMS !Following lines added from par_all36m_prot.prm -!MASS -1 H 1.00800 ! polar H -!MASS -1 HC 1.00800 ! N-ter H -!MASS -1 HA 1.00800 ! nonpolar H -!MASS -1 HP 1.00800 ! aromatic H -!MASS -1 HB1 1.00800 ! backbone H -!MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 -!MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 -!MASS -1 HR2 1.00800 ! (+) his HE1 -!MASS -1 HR3 1.00800 ! neutral his HG, HD2 -!MASS -1 HS 1.00800 ! thiol hydrogen -!MASS -1 HE1 1.00800 ! for alkene; RHC=CR -!MASS -1 HE2 1.00800 ! for alkene; H2C=CR -!MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 C 12.01100 ! carbonyl C, peptide backbone -!MASS -1 CA 12.01100 ! aromatic C -!MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters -!MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH -!MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 -!MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu -!MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 -!MASS -1 CPH1 12.01100 ! his CG and CD2 carbons -!MASS -1 CPH2 12.01100 ! his CE1 carbon -!MASS -1 CPT 12.01100 ! trp C between rings -!MASS -1 CY 12.01100 ! TRP C in pyrrole ring -!MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) -!MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) -!MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) -!MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 -!MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 -!MASS -1 CS 12.01100 ! thiolate carbon -!MASS -1 CE1 12.01100 ! for alkene; RHC=CR -!MASS -1 CE2 12.01100 ! for alkene; H2C=CR -!MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp -!MASS -1 C3 12.01100 ! cyclopropane carbon -!MASS -1 N 14.00700 ! proline N -!MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen -!MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen -!MASS -1 NR3 14.00700 ! charged his ring nitrogen -!MASS -1 NH1 14.00700 ! peptide nitrogen -!MASS -1 NH2 14.00700 ! amide nitrogen -!MASS -1 NH3 14.00700 ! ammonium nitrogen -!MASS -1 NC2 14.00700 ! guanidinium nitrogen -!MASS -1 NY 14.00700 ! TRP N in pyrrole ring -!MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) -!MASS -1 O 15.99900 ! carbonyl oxygen -!MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid -!MASS -1 OC 15.99900 ! carboxylate oxygen -!MASS -1 OH1 15.99900 ! hydroxyl oxygen -!MASS -1 OS 15.99940 ! ester oxygen -!MASS -1 S 32.06000 ! sulphur -!MASS -1 SM 32.06000 ! sulfur C-S-S-C type -!MASS -1 SS 32.06000 ! thiolate sulfur -! -! +MASS -1 H 1.00800 ! polar H +MASS -1 HC 1.00800 ! N-ter H +MASS -1 HA 1.00800 ! nonpolar H +MASS -1 HP 1.00800 ! aromatic H +MASS -1 HB1 1.00800 ! backbone H +MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS -1 HR2 1.00800 ! (+) his HE1 +MASS -1 HR3 1.00800 ! neutral his HG, HD2 +MASS -1 HS 1.00800 ! thiol hydrogen +MASS -1 HE1 1.00800 ! for alkene; RHC=CR +MASS -1 HE2 1.00800 ! for alkene; H2C=CR +MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 C 12.01100 ! carbonyl C, peptide backbone +MASS -1 CA 12.01100 ! aromatic C +MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters +MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH +MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu +MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS -1 CPH1 12.01100 ! his CG and CD2 carbons +MASS -1 CPH2 12.01100 ! his CE1 carbon +MASS -1 CPT 12.01100 ! trp C between rings +MASS -1 CY 12.01100 ! TRP C in pyrrole ring +MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) +MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) +MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS -1 CS 12.01100 ! thiolate carbon +MASS -1 CE1 12.01100 ! for alkene; RHC=CR +MASS -1 CE2 12.01100 ! for alkene; H2C=CR +MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp +MASS -1 C3 12.01100 ! cyclopropane carbon +MASS -1 N 14.00700 ! proline N +MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS -1 NR3 14.00700 ! charged his ring nitrogen +MASS -1 NH1 14.00700 ! peptide nitrogen +MASS -1 NH2 14.00700 ! amide nitrogen +MASS -1 NH3 14.00700 ! ammonium nitrogen +MASS -1 NC2 14.00700 ! guanidinium nitrogen +MASS -1 NY 14.00700 ! TRP N in pyrrole ring +MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS -1 O 15.99900 ! carbonyl oxygen +MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS -1 OC 15.99900 ! carboxylate oxygen +MASS -1 OH1 15.99900 ! hydroxyl oxygen +MASS -1 OS 15.99940 ! ester oxygen +MASS -1 S 32.06000 ! sulphur +MASS -1 SM 32.06000 ! sulfur C-S-S-C type +MASS -1 SS 32.06000 ! thiolate sulfur + + !Following lines added from par_water_ions.prm -!MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN -!MASS -1 HX 1.00800 ! hydroxide hydrogen -!MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN -!MASS -1 OX 15.99940 ! hydroxide oxygen -!MASS -1 HPER 1.00800 ! H of H2O2 -!MASS -1 OPER 15.99900 ! O of H2O2 -!MASS -1 LIT 6.94100 ! Lithium ion -!MASS -1 SOD 22.98977 ! Sodium Ion -!MASS -1 MG 24.30500 ! Magnesium Ion -!MASS -1 POT 39.09830 ! Potassium Ion -!MASS -1 CAL 40.08000 ! Calcium Ion -!MASS -1 RUB 85.46780 ! Rubidium Ion -!MASS -1 CES 132.90545 ! Cesium Ion -!MASS -1 BAR 137.32700 ! Barium Ion -!MASS -1 ZN 65.37000 ! zinc (II) cation -!MASS -1 CAD 112.41100 ! cadmium (II) cation -!MASS -1 CLA 35.45000 ! Chloride Ion -! +MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS -1 HX 1.00800 ! hydroxide hydrogen +MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS -1 OX 15.99940 ! hydroxide oxygen +MASS -1 HPER 1.00800 ! H of H2O2 +MASS -1 OPER 15.99900 ! O of H2O2 +MASS -1 LIT 6.94100 ! Lithium ion +MASS -1 SOD 22.98977 ! Sodium Ion +MASS -1 MG 24.30500 ! Magnesium Ion +MASS -1 POT 39.09830 ! Potassium Ion +MASS -1 CAL 40.08000 ! Calcium Ion +MASS -1 RUB 85.46780 ! Rubidium Ion +MASS -1 CES 132.90545 ! Cesium Ion +MASS -1 BAR 137.32700 ! Barium Ion +MASS -1 ZN 65.37000 ! zinc (II) cation +MASS -1 CAD 112.41100 ! cadmium (II) cation +MASS -1 CLA 35.45000 ! Chloride Ion + !Following lines added from par_all36_prot_arg0.prm -!MASS -1 HRA3 1.00800 ! alphatic proton, CH3 -!MASS -1 HRP2 1.00800 ! polar H, +ve charge -!MASS -1 HRM1 1.00800 ! polar H, dimethylamine -!MASS -1 HRM2 1.00800 ! polar H, methylamine -!MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium -!MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) -!MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base -!MASS -1 NRN1 14.00700 ! dimethylamine nitrogen -!MASS -1 NRN2 14.00700 ! methylamine nitrogen -! +MASS -1 HRA3 1.00800 ! alphatic proton, CH3 +MASS -1 HRP2 1.00800 ! polar H, +ve charge +MASS -1 HRM1 1.00800 ! polar H, dimethylamine +MASS -1 HRM2 1.00800 ! polar H, methylamine +MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium +MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) +MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base +MASS -1 NRN1 14.00700 ! dimethylamine nitrogen +MASS -1 NRN2 14.00700 ! methylamine nitrogen + !Following lines added from par_ions_won.prm !MASS -1 Li1p 6.94000 ! Lithium !MASS -1 Na1p 22.99000 ! Sodium !MASS -1 K1p 39.09000 ! Potassium !MASS -1 Rb1p 85.46000 ! Rubidium !MASS -1 Cs1p 132.91000 ! Cesium -!MASS -1 Cu1p 63.54600 ! Copper -!MASS -1 Ag1p 107.87000 ! Silver -!MASS -1 Au1p 196.97000 ! Gold -!MASS -1 Ti1p 47.86700 ! Titanium -!MASS -1 Be2p 9.01220 ! Beryllium +MASS -1 Cu1p 63.54600 ! Copper +MASS -1 Ag1p 107.87000 ! Silver +MASS -1 Au1p 196.97000 ! Gold +MASS -1 Ti1p 47.86700 ! Titanium +MASS -1 Be2p 9.01220 ! Beryllium !MASS -1 Mg2p 24.30500 ! Magnesium !MASS -1 Ca2p 40.07800 ! Calcium -!MASS -1 Sr2p 87.62000 ! Strontium +MASS -1 Sr2p 87.62000 ! Strontium !MASS -1 Ba2p 1 37.33 00 ! Barium -!MASS -1 Ra2p 226.03000 ! Radium -!MASS -1 V2p 50.94200 ! Vanadium -!MASS -1 Cr2p 51.99600 ! Chromium -!MASS -1 Mn2p 54.93800 ! Manganese -!MASS -1 Fe2p 55.85400 ! Iron -!MASS -1 Co2p 58.93300 ! Cobalt -!MASS -1 Ni2p 58.69300 ! Nickel -!MASS -1 Cu2p 63.54600 ! Copper +MASS -1 Ra2p 226.03000 ! Radium +MASS -1 V2p 50.94200 ! Vanadium +MASS -1 Cr2p 51.99600 ! Chromium +MASS -1 Mn2p 54.93800 ! Manganese +MASS -1 Fe2p 55.85400 ! Iron +MASS -1 Co2p 58.93300 ! Cobalt +MASS -1 Ni2p 58.69300 ! Nickel +MASS -1 Cu2p 63.54600 ! Copper !MASS -1 Zn2p 65.38000 ! Zinc -!MASS -1 Pd2p 106.42000 ! Palladium -!MASS -1 Ag2p 107.87000 ! Silver +MASS -1 Pd2p 106.42000 ! Palladium +MASS -1 Ag2p 107.87000 ! Silver !MASS -1 Cd2p 1 12.41000 ! Cadmium -!MASS -1 Sn2p 118.71000 ! Tin -!MASS -1 Pt2p 195.08000 ! Platinum -!MASS -1 Hg2p 200.59000 ! Mercury -!MASS -1 Pb2p 207.20000 ! Lead -!MASS -1 Sm2p 150.36000 ! Samarium -!MASS -1 Eu2p 151.96000 ! Europium -!MASS -1 Yb2p 173.05000 ! Ytterbium -!MASS -1 Al3p 26.98200 ! Aluminum -!MASS -1 Sc3p 44.95600 ! Scandium -!MASS -1 Y3p 88.90600 ! Yttrium -!MASS -1 La3p 138.91000 ! Lanthanum -!MASS -1 Ce3p 140.12000 ! Cerium -!MASS -1 Pr3p 140.91000 ! Praseodynium -!MASS -1 Nd3p 144.24000 ! Neodynium -!MASS -1 Pm3p 144.91000 ! Promethium -!MASS -1 Sm3p 150.36000 ! Samarium -!MASS -1 Eu3p 151.96000 ! Europium -!MASS -1 Gd3p 157.25000 ! Gadolinium -!MASS -1 Tb3p 158.93000 ! Terbium -!MASS -1 Dy3p 162.50000 ! Dysprosium -!MASS -1 Ho3p 164.93000 ! Holmium -!MASS -1 Er3p 167.28000 ! Erbium -!MASS -1 Tm3p 168.93000 ! Thulium -!MASS -1 Yb3p 173.05000 ! Ytterbium -!MASS -1 Lu3p 174.97000 ! Lutetium -!MASS -1 U3p 238.03000 ! Uranium -!MASS -1 Pu3p 244.06000 ! Plutonium -!MASS -1 Ti3p 47.86700 ! Titanium -!MASS -1 V3p 50.94200 ! Vanadium -!MASS -1 Cr3p 51.99600 ! Chromium -!MASS -1 Mn3p 54.93800 ! Manganese -!MASS -1 Fe3p 55.85400 ! Iron -!MASS -1 Co3p 58.93300 ! Cobalt -!MASS -1 Ga3p 69.72300 ! Gallium -!MASS -1 Rh3p 102.91000 ! Rhodium -!MASS -1 In3p 114.82000 ! Indium -!MASS -1 Au3p 196.97000 ! Gold -!MASS -1 Tl3p 204.38000 ! Thallium -!MASS -1 Bi3p 208.98000 ! Bismuth -! +MASS -1 Sn2p 118.71000 ! Tin +MASS -1 Pt2p 195.08000 ! Platinum +MASS -1 Hg2p 200.59000 ! Mercury +MASS -1 Pb2p 207.20000 ! Lead +MASS -1 Sm2p 150.36000 ! Samarium +MASS -1 Eu2p 151.96000 ! Europium +MASS -1 Yb2p 173.05000 ! Ytterbium +MASS -1 Al3p 26.98200 ! Aluminum +MASS -1 Sc3p 44.95600 ! Scandium +MASS -1 Y3p 88.90600 ! Yttrium +MASS -1 La3p 138.91000 ! Lanthanum +MASS -1 Ce3p 140.12000 ! Cerium +MASS -1 Pr3p 140.91000 ! Praseodynium +MASS -1 Nd3p 144.24000 ! Neodynium +MASS -1 Pm3p 144.91000 ! Promethium +MASS -1 Sm3p 150.36000 ! Samarium +MASS -1 Eu3p 151.96000 ! Europium +MASS -1 Gd3p 157.25000 ! Gadolinium +MASS -1 Tb3p 158.93000 ! Terbium +MASS -1 Dy3p 162.50000 ! Dysprosium +MASS -1 Ho3p 164.93000 ! Holmium +MASS -1 Er3p 167.28000 ! Erbium +MASS -1 Tm3p 168.93000 ! Thulium +MASS -1 Yb3p 173.05000 ! Ytterbium +MASS -1 Lu3p 174.97000 ! Lutetium +MASS -1 U3p 238.03000 ! Uranium +MASS -1 Pu3p 244.06000 ! Plutonium +MASS -1 Ti3p 47.86700 ! Titanium +MASS -1 V3p 50.94200 ! Vanadium +MASS -1 Cr3p 51.99600 ! Chromium +MASS -1 Mn3p 54.93800 ! Manganese +MASS -1 Fe3p 55.85400 ! Iron +MASS -1 Co3p 58.93300 ! Cobalt +MASS -1 Ga3p 69.72300 ! Gallium +MASS -1 Rh3p 102.91000 ! Rhodium +MASS -1 In3p 114.82000 ! Indium +MASS -1 Au3p 196.97000 ! Gold +MASS -1 Tl3p 204.38000 ! Thallium +MASS -1 Bi3p 208.98000 ! Bismuth + !standard C36 additive truncation BONDS !Following lines added from par_all36m_prot.prm @@ -3568,7 +3568,7 @@ C NH1 CT2 C NH1 CT2 C N 24 NONBONDED !Following lines added from par_all36m_prot.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 2013 correction ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] @@ -3685,7 +3685,7 @@ SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 !Following lines added from par_water_ions.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !TIP3P LJ parameters HT 0.0 -0.046 0.2245 @@ -3726,7 +3726,7 @@ CLA 0.0 -0.150 2.27 ! Chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol !Following lines added from par_all36_prot_arg0.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme !methylguanidine parameters HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 @@ -3742,9 +3742,8 @@ NRN1 0.0 -0.4500 2.0000 ! aliphatic amines NRN2 0.0 -0.0600 1.9900 ! aliphatic amines !end methylguanidine -!END !Following lines added from par_ions_won.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !truncation scheme used in JPCA 2012 paper under stochastic !boundary conditions. @@ -3820,7 +3819,6 @@ Au3p 0.0 -0.1330 0.3654 ! dA = -4420 kJ/mol Tl3p 0.0 -0.1629 0.8693 ! dA = -3970 kJ/mol Bi3p 0.0 -0.1850 1.3682 ! dA = -3480 kJ/mol -!END NBFIX !Following lines added from par_all36m_prot.prm ! Emin Rmin @@ -3832,7 +3830,6 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! (kcal/mol) (A) !SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 !POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189, repeated below -!END ! The following section contains NBFixes for sodium interacting with ! carboxylate oxygens of various CHARMM force fields. It will generate @@ -3845,12 +3842,12 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! want the NBFixes to apply. A more elegant solution would require new ! features to be added to CHARMM. ! parallel fix, to avoid duplicated messages in the log -!set para -!if ?NUMNODE gt 1 set para node 0 +set para +if ?NUMNODE gt 1 set para node 0 -!set wrn ?WRNLEV +set wrn ?WRNLEV ! Some versions of CHARMM don't seem to initialize wrnlev... -!if "@WRN" eq "?WRNLEV" set wrn 5 +if "@WRN" eq "?WRNLEV" set wrn 5 HBOND !Following lines added from par_all36m_prot.prm ! READ PARAM APPEND CARD diff --git a/test-charmm-build/3PTB_insertion/parameters b/test-charmm-build/3PTB_insertion/parameters index f667868..6dc1448 100644 --- a/test-charmm-build/3PTB_insertion/parameters +++ b/test-charmm-build/3PTB_insertion/parameters @@ -5,7 +5,7 @@ * All comments to the CHARMM web site: www.charmm.org * parameter set discussion forum * -! + !references ! !Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M, de Groot, B.L., @@ -32,169 +32,169 @@ !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. -! + * Parameters for water and ions * -! -! + + * par_cation.prm for mono-, di-, and trivalent cations * -! -!ATOMS + +ATOMS !Following lines added from par_all36m_prot.prm -!MASS -1 H 1.00800 ! polar H -!MASS -1 HC 1.00800 ! N-ter H -!MASS -1 HA 1.00800 ! nonpolar H -!MASS -1 HP 1.00800 ! aromatic H -!MASS -1 HB1 1.00800 ! backbone H -!MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 -!MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 -!MASS -1 HR2 1.00800 ! (+) his HE1 -!MASS -1 HR3 1.00800 ! neutral his HG, HD2 -!MASS -1 HS 1.00800 ! thiol hydrogen -!MASS -1 HE1 1.00800 ! for alkene; RHC=CR -!MASS -1 HE2 1.00800 ! for alkene; H2C=CR -!MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) -!MASS -1 C 12.01100 ! carbonyl C, peptide backbone -!MASS -1 CA 12.01100 ! aromatic C -!MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters -!MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH -!MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 -!MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu -!MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 -!MASS -1 CPH1 12.01100 ! his CG and CD2 carbons -!MASS -1 CPH2 12.01100 ! his CE1 carbon -!MASS -1 CPT 12.01100 ! trp C between rings -!MASS -1 CY 12.01100 ! TRP C in pyrrole ring -!MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) -!MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) -!MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) -!MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 -!MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 -!MASS -1 CS 12.01100 ! thiolate carbon -!MASS -1 CE1 12.01100 ! for alkene; RHC=CR -!MASS -1 CE2 12.01100 ! for alkene; H2C=CR -!MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp -!MASS -1 C3 12.01100 ! cyclopropane carbon -!MASS -1 N 14.00700 ! proline N -!MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen -!MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen -!MASS -1 NR3 14.00700 ! charged his ring nitrogen -!MASS -1 NH1 14.00700 ! peptide nitrogen -!MASS -1 NH2 14.00700 ! amide nitrogen -!MASS -1 NH3 14.00700 ! ammonium nitrogen -!MASS -1 NC2 14.00700 ! guanidinium nitrogen -!MASS -1 NY 14.00700 ! TRP N in pyrrole ring -!MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) -!MASS -1 O 15.99900 ! carbonyl oxygen -!MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid -!MASS -1 OC 15.99900 ! carboxylate oxygen -!MASS -1 OH1 15.99900 ! hydroxyl oxygen -!MASS -1 OS 15.99940 ! ester oxygen -!MASS -1 S 32.06000 ! sulphur -!MASS -1 SM 32.06000 ! sulfur C-S-S-C type -!MASS -1 SS 32.06000 ! thiolate sulfur -! -! +MASS -1 H 1.00800 ! polar H +MASS -1 HC 1.00800 ! N-ter H +MASS -1 HA 1.00800 ! nonpolar H +MASS -1 HP 1.00800 ! aromatic H +MASS -1 HB1 1.00800 ! backbone H +MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS -1 HR2 1.00800 ! (+) his HE1 +MASS -1 HR3 1.00800 ! neutral his HG, HD2 +MASS -1 HS 1.00800 ! thiol hydrogen +MASS -1 HE1 1.00800 ! for alkene; RHC=CR +MASS -1 HE2 1.00800 ! for alkene; H2C=CR +MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 C 12.01100 ! carbonyl C, peptide backbone +MASS -1 CA 12.01100 ! aromatic C +MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters +MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH +MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu +MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS -1 CPH1 12.01100 ! his CG and CD2 carbons +MASS -1 CPH2 12.01100 ! his CE1 carbon +MASS -1 CPT 12.01100 ! trp C between rings +MASS -1 CY 12.01100 ! TRP C in pyrrole ring +MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) +MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) +MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS -1 CS 12.01100 ! thiolate carbon +MASS -1 CE1 12.01100 ! for alkene; RHC=CR +MASS -1 CE2 12.01100 ! for alkene; H2C=CR +MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp +MASS -1 C3 12.01100 ! cyclopropane carbon +MASS -1 N 14.00700 ! proline N +MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS -1 NR3 14.00700 ! charged his ring nitrogen +MASS -1 NH1 14.00700 ! peptide nitrogen +MASS -1 NH2 14.00700 ! amide nitrogen +MASS -1 NH3 14.00700 ! ammonium nitrogen +MASS -1 NC2 14.00700 ! guanidinium nitrogen +MASS -1 NY 14.00700 ! TRP N in pyrrole ring +MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS -1 O 15.99900 ! carbonyl oxygen +MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS -1 OC 15.99900 ! carboxylate oxygen +MASS -1 OH1 15.99900 ! hydroxyl oxygen +MASS -1 OS 15.99940 ! ester oxygen +MASS -1 S 32.06000 ! sulphur +MASS -1 SM 32.06000 ! sulfur C-S-S-C type +MASS -1 SS 32.06000 ! thiolate sulfur + + !Following lines added from par_water_ions.prm -!MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN -!MASS -1 HX 1.00800 ! hydroxide hydrogen -!MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN -!MASS -1 OX 15.99940 ! hydroxide oxygen -!MASS -1 HPER 1.00800 ! H of H2O2 -!MASS -1 OPER 15.99900 ! O of H2O2 -!MASS -1 LIT 6.94100 ! Lithium ion -!MASS -1 SOD 22.98977 ! Sodium Ion -!MASS -1 MG 24.30500 ! Magnesium Ion -!MASS -1 POT 39.09830 ! Potassium Ion -!MASS -1 CAL 40.08000 ! Calcium Ion -!MASS -1 RUB 85.46780 ! Rubidium Ion -!MASS -1 CES 132.90545 ! Cesium Ion -!MASS -1 BAR 137.32700 ! Barium Ion -!MASS -1 ZN 65.37000 ! zinc (II) cation -!MASS -1 CAD 112.41100 ! cadmium (II) cation -!MASS -1 CLA 35.45000 ! Chloride Ion -! +MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN +MASS -1 HX 1.00800 ! hydroxide hydrogen +MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN +MASS -1 OX 15.99940 ! hydroxide oxygen +MASS -1 HPER 1.00800 ! H of H2O2 +MASS -1 OPER 15.99900 ! O of H2O2 +MASS -1 LIT 6.94100 ! Lithium ion +MASS -1 SOD 22.98977 ! Sodium Ion +MASS -1 MG 24.30500 ! Magnesium Ion +MASS -1 POT 39.09830 ! Potassium Ion +MASS -1 CAL 40.08000 ! Calcium Ion +MASS -1 RUB 85.46780 ! Rubidium Ion +MASS -1 CES 132.90545 ! Cesium Ion +MASS -1 BAR 137.32700 ! Barium Ion +MASS -1 ZN 65.37000 ! zinc (II) cation +MASS -1 CAD 112.41100 ! cadmium (II) cation +MASS -1 CLA 35.45000 ! Chloride Ion + !Following lines added from par_all36_prot_arg0.prm -!MASS -1 HRA3 1.00800 ! alphatic proton, CH3 -!MASS -1 HRP2 1.00800 ! polar H, +ve charge -!MASS -1 HRM1 1.00800 ! polar H, dimethylamine -!MASS -1 HRM2 1.00800 ! polar H, methylamine -!MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium -!MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) -!MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base -!MASS -1 NRN1 14.00700 ! dimethylamine nitrogen -!MASS -1 NRN2 14.00700 ! methylamine nitrogen -! +MASS -1 HRA3 1.00800 ! alphatic proton, CH3 +MASS -1 HRP2 1.00800 ! polar H, +ve charge +MASS -1 HRM1 1.00800 ! polar H, dimethylamine +MASS -1 HRM2 1.00800 ! polar H, methylamine +MASS -1 CRN1 12.01100 ! conjugated C in Arg/guanidinium +MASS -1 CR33 12.01100 ! aliphatic C for methyl group (-CH3) +MASS -1 NRC4 14.00700 ! N for deprotonated Schiff's base +MASS -1 NRN1 14.00700 ! dimethylamine nitrogen +MASS -1 NRN2 14.00700 ! methylamine nitrogen + !Following lines added from par_ions_won.prm !MASS -1 Li1p 6.94000 ! Lithium !MASS -1 Na1p 22.99000 ! Sodium !MASS -1 K1p 39.09000 ! Potassium !MASS -1 Rb1p 85.46000 ! Rubidium !MASS -1 Cs1p 132.91000 ! Cesium -!MASS -1 Cu1p 63.54600 ! Copper -!MASS -1 Ag1p 107.87000 ! Silver -!MASS -1 Au1p 196.97000 ! Gold -!MASS -1 Ti1p 47.86700 ! Titanium -!MASS -1 Be2p 9.01220 ! Beryllium +MASS -1 Cu1p 63.54600 ! Copper +MASS -1 Ag1p 107.87000 ! Silver +MASS -1 Au1p 196.97000 ! Gold +MASS -1 Ti1p 47.86700 ! Titanium +MASS -1 Be2p 9.01220 ! Beryllium !MASS -1 Mg2p 24.30500 ! Magnesium !MASS -1 Ca2p 40.07800 ! Calcium -!MASS -1 Sr2p 87.62000 ! Strontium +MASS -1 Sr2p 87.62000 ! Strontium !MASS -1 Ba2p 1 37.33 00 ! Barium -!MASS -1 Ra2p 226.03000 ! Radium -!MASS -1 V2p 50.94200 ! Vanadium -!MASS -1 Cr2p 51.99600 ! Chromium -!MASS -1 Mn2p 54.93800 ! Manganese -!MASS -1 Fe2p 55.85400 ! Iron -!MASS -1 Co2p 58.93300 ! Cobalt -!MASS -1 Ni2p 58.69300 ! Nickel -!MASS -1 Cu2p 63.54600 ! Copper +MASS -1 Ra2p 226.03000 ! Radium +MASS -1 V2p 50.94200 ! Vanadium +MASS -1 Cr2p 51.99600 ! Chromium +MASS -1 Mn2p 54.93800 ! Manganese +MASS -1 Fe2p 55.85400 ! Iron +MASS -1 Co2p 58.93300 ! Cobalt +MASS -1 Ni2p 58.69300 ! Nickel +MASS -1 Cu2p 63.54600 ! Copper !MASS -1 Zn2p 65.38000 ! Zinc -!MASS -1 Pd2p 106.42000 ! Palladium -!MASS -1 Ag2p 107.87000 ! Silver +MASS -1 Pd2p 106.42000 ! Palladium +MASS -1 Ag2p 107.87000 ! Silver !MASS -1 Cd2p 1 12.41000 ! Cadmium -!MASS -1 Sn2p 118.71000 ! Tin -!MASS -1 Pt2p 195.08000 ! Platinum -!MASS -1 Hg2p 200.59000 ! Mercury -!MASS -1 Pb2p 207.20000 ! Lead -!MASS -1 Sm2p 150.36000 ! Samarium -!MASS -1 Eu2p 151.96000 ! Europium -!MASS -1 Yb2p 173.05000 ! Ytterbium -!MASS -1 Al3p 26.98200 ! Aluminum -!MASS -1 Sc3p 44.95600 ! Scandium -!MASS -1 Y3p 88.90600 ! Yttrium -!MASS -1 La3p 138.91000 ! Lanthanum -!MASS -1 Ce3p 140.12000 ! Cerium -!MASS -1 Pr3p 140.91000 ! Praseodynium -!MASS -1 Nd3p 144.24000 ! Neodynium -!MASS -1 Pm3p 144.91000 ! Promethium -!MASS -1 Sm3p 150.36000 ! Samarium -!MASS -1 Eu3p 151.96000 ! Europium -!MASS -1 Gd3p 157.25000 ! Gadolinium -!MASS -1 Tb3p 158.93000 ! Terbium -!MASS -1 Dy3p 162.50000 ! Dysprosium -!MASS -1 Ho3p 164.93000 ! Holmium -!MASS -1 Er3p 167.28000 ! Erbium -!MASS -1 Tm3p 168.93000 ! Thulium -!MASS -1 Yb3p 173.05000 ! Ytterbium -!MASS -1 Lu3p 174.97000 ! Lutetium -!MASS -1 U3p 238.03000 ! Uranium -!MASS -1 Pu3p 244.06000 ! Plutonium -!MASS -1 Ti3p 47.86700 ! Titanium -!MASS -1 V3p 50.94200 ! Vanadium -!MASS -1 Cr3p 51.99600 ! Chromium -!MASS -1 Mn3p 54.93800 ! Manganese -!MASS -1 Fe3p 55.85400 ! Iron -!MASS -1 Co3p 58.93300 ! Cobalt -!MASS -1 Ga3p 69.72300 ! Gallium -!MASS -1 Rh3p 102.91000 ! Rhodium -!MASS -1 In3p 114.82000 ! Indium -!MASS -1 Au3p 196.97000 ! Gold -!MASS -1 Tl3p 204.38000 ! Thallium -!MASS -1 Bi3p 208.98000 ! Bismuth -! +MASS -1 Sn2p 118.71000 ! Tin +MASS -1 Pt2p 195.08000 ! Platinum +MASS -1 Hg2p 200.59000 ! Mercury +MASS -1 Pb2p 207.20000 ! Lead +MASS -1 Sm2p 150.36000 ! Samarium +MASS -1 Eu2p 151.96000 ! Europium +MASS -1 Yb2p 173.05000 ! Ytterbium +MASS -1 Al3p 26.98200 ! Aluminum +MASS -1 Sc3p 44.95600 ! Scandium +MASS -1 Y3p 88.90600 ! Yttrium +MASS -1 La3p 138.91000 ! Lanthanum +MASS -1 Ce3p 140.12000 ! Cerium +MASS -1 Pr3p 140.91000 ! Praseodynium +MASS -1 Nd3p 144.24000 ! Neodynium +MASS -1 Pm3p 144.91000 ! Promethium +MASS -1 Sm3p 150.36000 ! Samarium +MASS -1 Eu3p 151.96000 ! Europium +MASS -1 Gd3p 157.25000 ! Gadolinium +MASS -1 Tb3p 158.93000 ! Terbium +MASS -1 Dy3p 162.50000 ! Dysprosium +MASS -1 Ho3p 164.93000 ! Holmium +MASS -1 Er3p 167.28000 ! Erbium +MASS -1 Tm3p 168.93000 ! Thulium +MASS -1 Yb3p 173.05000 ! Ytterbium +MASS -1 Lu3p 174.97000 ! Lutetium +MASS -1 U3p 238.03000 ! Uranium +MASS -1 Pu3p 244.06000 ! Plutonium +MASS -1 Ti3p 47.86700 ! Titanium +MASS -1 V3p 50.94200 ! Vanadium +MASS -1 Cr3p 51.99600 ! Chromium +MASS -1 Mn3p 54.93800 ! Manganese +MASS -1 Fe3p 55.85400 ! Iron +MASS -1 Co3p 58.93300 ! Cobalt +MASS -1 Ga3p 69.72300 ! Gallium +MASS -1 Rh3p 102.91000 ! Rhodium +MASS -1 In3p 114.82000 ! Indium +MASS -1 Au3p 196.97000 ! Gold +MASS -1 Tl3p 204.38000 ! Thallium +MASS -1 Bi3p 208.98000 ! Bismuth + !standard C36 additive truncation BONDS !Following lines added from par_all36m_prot.prm @@ -3568,7 +3568,7 @@ C NH1 CT2 C NH1 CT2 C N 24 NONBONDED !Following lines added from par_all36m_prot.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 2013 correction ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] @@ -3685,7 +3685,7 @@ SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 !Following lines added from par_water_ions.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !TIP3P LJ parameters HT 0.0 -0.046 0.2245 @@ -3726,7 +3726,7 @@ CLA 0.0 -0.150 2.27 ! Chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol !Following lines added from par_all36_prot_arg0.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme !methylguanidine parameters HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 @@ -3742,9 +3742,8 @@ NRN1 0.0 -0.4500 2.0000 ! aliphatic amines NRN2 0.0 -0.0600 1.9900 ! aliphatic amines !end methylguanidine -!END !Following lines added from par_ions_won.prm -!cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !truncation scheme used in JPCA 2012 paper under stochastic !boundary conditions. @@ -3820,7 +3819,6 @@ Au3p 0.0 -0.1330 0.3654 ! dA = -4420 kJ/mol Tl3p 0.0 -0.1629 0.8693 ! dA = -3970 kJ/mol Bi3p 0.0 -0.1850 1.3682 ! dA = -3480 kJ/mol -!END NBFIX !Following lines added from par_all36m_prot.prm ! Emin Rmin @@ -3832,7 +3830,6 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! (kcal/mol) (A) !SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 !POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189, repeated below -!END ! The following section contains NBFixes for sodium interacting with ! carboxylate oxygens of various CHARMM force fields. It will generate @@ -3845,12 +3842,12 @@ NC2 OC -0.154919 3.637 ! From osmotic pressure calibration ! want the NBFixes to apply. A more elegant solution would require new ! features to be added to CHARMM. ! parallel fix, to avoid duplicated messages in the log -!set para -!if ?NUMNODE gt 1 set para node 0 +set para +if ?NUMNODE gt 1 set para node 0 -!set wrn ?WRNLEV +set wrn ?WRNLEV ! Some versions of CHARMM don't seem to initialize wrnlev... -!if "@WRN" eq "?WRNLEV" set wrn 5 +if "@WRN" eq "?WRNLEV" set wrn 5 HBOND !Following lines added from par_all36m_prot.prm ! READ PARAM APPEND CARD