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Update charmm tests
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stefdoerr committed Nov 6, 2023
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311 changes: 154 additions & 157 deletions test-charmm-build/1A25/parameters
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Expand Up @@ -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.,
Expand All @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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.
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down
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