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parameters
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* Combined parameter file generated from par_all35_ethers.prm par_all36_carb.prm par_all36_lipid.prm par_all36_na.prm par_all36_prot.prm par_all36_water_ions.prm
* Date: Tue Jul 31 17:21:51 2012
* Script version: $Id: combine_parameters.pl 671 2011-01-31 18:44:22Z toni $
! (Following lines from par_all35_ethers.prm)
*>>>>>>>>>>>>>>>>> All-hydrogen parameters <<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>>>>>>>>>>> CHARMM32 ether force field <<<<<<<<<<<<<<<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>> December 2006 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<<
*>>>>>>>>>>>> via the CHARMM forum: www.charmm.org <<<<<<<<<<<<<<<
*
!Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A.,
!Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude
!Polarizable Force Fields for Linear and Cyclic Ethers," Journal of
!Chemical Theory and Computing, 3: 1120-1133, 2007
!
! O-C-C-O torsion modified; HK Lee, RM Venable, RW Pastor August 2007
!
!Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor
!Molecular dynamics studies of polyethylene oxide and polyethylene glycol:
!Hydrodynamic radius and shape anisotropy
!Biophysical J., 95: 1590-1599, 2008
!
! ********* V(bond) = Kb(b - b0)**2
! (Following lines from par_all35_ethers.prm)
* $Id: par_allxx_sugar.inp,v 1.126 2011-03-31 19:17:35 oguvench Exp $
*>>>>>>>>>>>> All-hydrogen parameters used in the <<<<<<<<<<<<<<<<
*>>>>> development of the CHARMM carbohydrate force field<<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>>>> June 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<<
*>>>>>>>>>> via the CHARMM web site: www.charmm.org <<<<<<<<<<<<<<
*>>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<<
*
! please reference the following:
! pyranose monosaccharides
!Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M.,
!Pastor, R.W., MacKerell, Jr., A.D. "Additive empirical force field for
!hexopyranose monosaccharides," Journal of Computational Chemistry, 29:
!2543-2564, 2008. PMID: 18470966
! linear sugars, sugar alcohols, and inositol
!Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. "CHARMM Additive
!All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates
!and Inositol," Journal of Chemical Theory and Computation, 5:
!1315-1327, 2009, DOI: 10.1021/ct9000608.
! hexopyranose glycosidic linkages
!Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, Jr.,
!A. D. "Additive Empirical CHARMM Force Field for glycosyl linked
!hexopyranoses," Journal of Chemical Theory and Computation, 5,
!2353-2370, 2009, DOI: 10.1021/ct900242e
! furanose monosaccharides
!Hatcher, E. R.; Guvench, O. and MacKerell, Jr., A.D.
!"CHARMM Additive All-Atom Force Field for Aldopentofuranose
! Carbohydrates and Fructofuranose." Journal of Physical Chemistry B.
! 113:12466-76, 2009, PMID: 19694450
! glycosidic linkages involving furanoses
!Raman, E. P., Guvench, O., MacKerell, Jr., A.D., "CHARMM Additive All-Atom
!Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses,"
!Journal of Physical Chemistry B, 114: 12981-12994, 2010, PMID: 20845956
! carbohydrate derivatives and glycosidic linkages for glycoproteins
!Guvench, O.; Mallajosyula, S. S.; Raman, E. P.; Hatcher, E. R.;
!Vanommeslaeghe, K.; Foster, T. J.; Jamison, F. W. and MacKerell, Jr., A.D.,
!"CHARMM additive all-atom force field for carbohydrate derivatives and its
!utility in polysaccharide and carbohydrate-protein modeling,"
!Journal of Chemical Theory and Computation, (In Press, 2011), DOI: 10.1021/ct200328p
!O-glycan linkages
!Mallajosyula, S. S. and MacKerell, Jr., A.D., "Influence of Solvent and
!Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked
!Glycopeptides," Journal of Physical Chemistry B, (In Press, 2011),
!DOI: 10.1021/jp203695t
! Phosphates and sulfates
! Mallajosyula, S. S.; Guvench, O.; Hatcher, E. R. and MacKerell, Jr., A.D.,
!"CHARMM Additive All-Atom Force Field for Phosphate and Sufate Linkages in
!Carbohydrates" Manuscript under preparation, 2011
! adm: Alex MacKerell
! sng: Shannon Greene
! og: Olgun Guvench
! erh: Elizabeth Hatcher
! rmv: Rick Venable
! viv: Igor Vorobyov
! pram: E.Prabhu Raman
! sai: Sairam S. Mallajosyula
! par22: par_all22_prot.inp
! par27: par_all27_lipid.prm
! par35: par_all35_ethers.prm
! (Following lines from par_all36_carb.prm)
* \\\\\\\ CHARMM36 All-Hydrogen Lipid Parameter File ///////
* All comments and questions should be submitted to the
* parameter forum at the CHARMM website: www.charmm.org
*
!references
!
!Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph
!W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor
!Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of
!the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six
!Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843
!
! PUFA Modifications
!Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving
!the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B.
!2012 ASAP http://dx.doi.org/10.1021/jp304056p
! (Following lines from par_all36_lipid.prm)
* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Parameter File ////
* Alexander D. MacKerell Jr. and coworkers
* April 2011
* All comments to the CHARMM web site: www.charmm.org parameter
* set discussion forum
*
!2010/2011 additions
! ejd, 2010 RNA update
! adm, 2011 DNA update
! For DNA update, new atom type required for P of DNA. This required
! replication of a number of parameters and the creation of new
! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
! CHARMM scripts to generate DNA will no longer work. Note that the
! atom type change to P3 ONLY applies to the phosphodester linkage in
! DNA and NOT to terminal phosphates, DMP etc.
!
!
!references
!
!NUCLEIC ACIDS
!
!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and
!MacKerell Jr., A.D. “Optimization of the CHARMM additive force field
!for DNA: Improved treatment of the BI/BII conformational
!equilibrium,” Journal of Chemical Theory and Computation, 8:348–362,
!2012, http://dx.doi.org/10.1021/ct200723y
!
!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
!“Impact of 2’-hydroxyl sampling on the conformational properties of
!RNA: Update of the CHARMM all-atom additive force field for RNA,”
!JCC, In Press, 2011, NIHMSID #272247
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
!
!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
!and RNA in Solution. JCC, 2000, 21: 105-120.
!
! (Following lines from par_all36_na.prm)
*>>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>>>>> Feb. 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
!references
!
!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P.
!Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization of the
!additive CHARMM all-atom protein force field targeting improved
!sampling of the backbone phi, psi and sidechain chi1 and chi2
!dihedral angles. In preparation
!
!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved
!treatment of the protein backbone in empirical force fields," Journal
!of the American Chemical Society, 126: 698-699, 2004
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!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.
! (Following lines from par_all36_prot.prm)
* Parameters for water and ions
*
! (Following lines from par_all36_water_ions.prm)
! The following section contains NBFixes for sodium interacting with
! carboxylate oxygens of various CHARMM force fields. It will generate
! level -1 warnings whenever any of these force fields have not been
! read prior to the current stream file. Since we don't want to force
! the user to always read all the force fields, we're suppressing the
! warnings. The only side effect is that you will have "most severe
! warning was at level 0" at the end of your output. Also note that
! the user is responsible for reading the current file last if they
! 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 wrn ?WRNLEV
!! Some versions of CHARMM don't seem to initialize wrnlev...
!if "@WRN" eq "?WRNLEV" set wrn 5
!set bom ?bomlev
!WRNLEV -1 @PARA
!BOMLEV -1 @PARA
!read para card flex append
* NBFix between carboxylate and sodium
*
! These NBFixes will only apply if the main files have been read in first!!!
! (Following lines from par_all36_water_ions.prm)
! The following flexible-parameters section was removed by combine-parameters.pl
! ATOM
! ! (Following lines from par_all35_ethers.prm)
! MASS 241 HCA1A 1.00800 ! Alkane H attached to C(sp3)H (eq. HA1)
! MASS 242 HCA2A 1.00800 ! Alkane H attached to C(sp3)H2 (eq. HA2)
! MASS 243 HCA3A 1.00800 ! Alkane H attached to C(sp3)H3 (eq. HA3)
! MASS 244 HCA25A 1.00800 ! Alkane H attached to C(sp3)H2 in 5-membered ring
! MASS 245 CC30A 12.01100 ! -C(sp3) Carbon (eq. CT)
! MASS 246 CC31A 12.01100 ! -C(sp3)H Carbon (eq. CT1)
! MASS 247 CC32A 12.01100 ! -C(sp3)H2 Carbon (eq. CT2)
! MASS 248 CC33A 12.01100 ! -C(sp3)H3 Carbon (eq. CT3)
! MASS 249 CC325A 12.01100 ! -C(sp3)H2 Carbon in 5-membered ring
! MASS 250 CC325B 12.01100 ! -C(sp3)H2 Carbon in THF (tetrahydrofuran)
! MASS 251 CC326A 12.01100 ! -C(sp3)H2 Carbon in THP (tetrahydropyran)
! MASS 252 OC30A 15.99940 ! Ether Oxygen
! MASS 253 OC305A 15.99940 ! Ether Oxygen in THF
!
! ! (Following lines from par_all36_carb.prm)
! ! tip3p water
! !MASS 1 HCTIP3 1.00800 ! TIP3P water hydrogen
! !MASS 2 OCTIP3 15.99940 ! TIP3P water oxygen
!
! ! C6H12O6 pyranose monosaccharide atom types
! MASS 171 CC301 12.01100 ! aliphatic C, no H's
! MASS 172 CC311 12.01100 ! generic acyclic CH carbon
! MASS 173 CC312 12.01100 ! CH carbon in linear polyols
! MASS 174 CC3161 12.01100 ! C2, C3, C4 CH bound to OH
! MASS 175 CC3162 12.01100 ! C1 (anomeric) CH bound to OH
! MASS 176 CC3163 12.01100 ! C5 CH bound to exocylic CH2OH
! MASS 177 CC321 12.01100 ! generic acyclic CH2 carbon (hexopyranose C6)
! MASS 178 CC322 12.01100 ! CH2 carbon in linear polyols erh
! MASS 179 CC3263 12.01100 ! C5 in xylose
! MASS 180 CC331 12.01100 ! generic acyclic CH3 carbon (xyl C6, glcna/galna CT)
! MASS 181 CC2O1 12.01100 ! sp2 carbon in amides, aldoses
! MASS 182 CC2O2 12.01100 ! sp2 carbon in carboxylates
! MASS 183 CC2O3 12.01100 ! sp2 carbon in acetone, ketoses
! MASS 184 CC2O4 12.01100 ! c22 CD
! MASS 185 HCA1 1.00800 ! aliphatic proton, CH
! MASS 186 HCA2 1.00800 ! aliphatic proton, CH2
! MASS 187 HCA3 1.00800 ! aliphatic proton, CH3
! MASS 188 HCP1 1.00800 ! polar H
! MASS 189 HCR1 1.00800 ! c22 HR1
! MASS 191 OC311 15.99940 ! hydroxyl oxygen
! MASS 192 OC3C61 15.99940 ! ether in six membered ring
! MASS 193 OC301 15.99940 ! generic linear ether
! MASS 194 OC302 15.99940 ! linear ether in 1-1 glycosidic linkage
! MASS 195 OC2D1 15.99940 ! sp2 oxygen in amides, aldoses
! MASS 196 OC2D2 15.99940 ! sp2 oxygen in carboxylates
! MASS 197 OC2D3 15.99940 ! sp2 oxygen in acetone, ketoses
! MASS 198 OC2D4 15.99940 ! par22 O
! MASS 200 NC2D1 14.00700 ! peptide, NMA, IPAA nitrogen (C=NHR)
! ! model compound atom types
! MASS 201 CC321C 12.01100 ! cyclohexane, thp CH2
! MASS 202 HCA3M 1.00800 ! alcohol aliphatic proton, CH3
! MASS 203 HCP1M 1.00800 ! EGLY hydroxyl H
! MASS 204 OC311M 15.99940 ! MEOH, ETOH, PRO2, EGLY hydroxyl O
! MASS 205 CC321D 12.01100 ! cyclohexane, thp CH2 model for 1-1 linkage
! MASS 206 CC311C 12.01100 ! patch C1 in model compound
! MASS 207 CC311D 12.01100 ! patch C1 in model compound
! ! THF atom types
! MASS 208 OC3C5M 15.99940 ! thf ring oxygen
! MASS 209 CC322C 12.01100 ! cyclopentane, thf CH2
! MASS 210 HCA2C2 1.00800 ! cyclopentane, thp aliphatic proton, CH2
! MASS 211 CC312C 12.01100 ! tf2m CH1
! MASS 212 HCA1C2 1.00800 ! tf2m aliphatic proton, CH1
! ! Furanose atom types; erh 10/24/07
! MASS 213 OC3C51 15.99940 ! furan ring oxygen
! MASS 214 CC3152 12.01100 ! furan ring carbon
! MASS 215 CC3153 12.01100 ! furan ring carbon
! MASS 216 CC3251 12.01100 ! furan ring carbon; C2 deoxy
! MASS 217 CC3151 12.01100 ! furan ring carbon
! MASS 218 CC3051 12.01100 ! furan ring carbon; C2 fructose
! ! pyranose derivatives
! MASS 219 CC3062 12.01100 ! C2 on NE5AC
! MASS 220 CC3261 12.01100 ! C3 on NE5AC
! !dummy atom
! !MASS 99 DUM 1.00800 H ! dummy atom
!
! !Added by sai for modelling phosphate
! MASS 221 OC312 15.99940 ! OH in PO3H (phosphate) || OHL in top_all27_lipid.rtf
! MASS 222 OC30P 15.99940 ! ester O in PO3H (phosphate) || OSL in top_all27_lipid.rtf
! MASS 223 OC2DP 15.99940 ! =0 in P03H (phosphate) || O2L in top_all27_lipid.rtf
! MASS 224 PC 30.97400 ! phosphorus || PL in top_all27_lipid.rtf
! MASS 225 SC 32.06000 ! Sulfate sulfur
!
! !pram, furanosyl linkages
! MASS 226 CC312D 12.01100 ! from CC322C; THF anomeric carbon
! MASS 227 OC303 15.99940 ! from OC301; linear ether in P1->F3 pyranose-furanose glycosidic linkage
!
! ! (Following lines from par_all36_lipid.prm)
! MASS 136 HL 1.008000 ! polar H (equivalent to protein H)
! MASS 137 HCL 1.008000 ! charged H for PE (equivalent to protein HC)
! MASS 138 HOL 1.008000 ! Nucleic acid phosphate hydroxyl proton
! MASS 139 HAL1 1.008000 ! alphatic proton
! MASS 140 HAL2 1.008000 ! alphatic proton
! MASS 141 HAL3 1.008000 ! alphatic proton
! MASS 142 HEL1 1.008000 ! for alkene; RHC=CR
! MASS 143 HEL2 1.008000 ! for alkene; H2C=CR
! MASS 144 HBL 1.008000 ! POPS SER backbone H
! MASS 145 CL 12.011000 ! carbonyl C (acetic acid/methyl acetate)
! MASS 146 CTL1 12.011000 ! sp3 carbon with 1 H (-CH1-)
! MASS 147 CTL2 12.011000 ! carbon of methylene group (-CH2-)
! MASS 148 CTL3 12.011000 ! carbon of methyl group (-CH3)
! MASS 149 CTL5 12.011000 ! carbon of methyl group (-CH3) for tetramethylammonium
! MASS 150 CEL1 12.011000 ! for alkene; RHC=CR
! MASS 151 CEL2 12.011000 ! for alkene; H2C=CR
! MASS 152 CCL 12.011000 ! for POPS
! MASS 153 NTL 14.007000 ! ammonium nitrogen
! MASS 154 NH3L 14.007000 ! nitrogen phosphatidylethanolamine
! MASS 155 OBL 15.999400 ! acetic acid carboxyl oxygen (e. to protein OB)
! MASS 156 OCL 15.999400 ! acetate oxygen
! MASS 157 OSL 15.999400 ! ester oxygen
! MASS 158 O2L 15.999400 ! Nucleic acid =O in phosphate or sulfate
! MASS 159 OHL 15.999400 ! Nucleic acid phosphate hydroxyl oxygen
! MASS 160 OSLP 15.999400 ! Phosphate oxygen, to avoid conflict with methylacetate type O
! MASS 161 PL 30.974000 ! phosphorus
! MASS 162 SL 32.060000 ! Sulfate sulfur
! MASS 163 CRL1 12.011000 ! sp3 carbon with 1 H on a ring (-CH1-) for sterols
! MASS 164 CRL2 12.011000 ! carbon of methylene group on a ring (-CH2-) for sterols
!
! ! (Following lines from par_all36_na.prm)
! MASS 91 HN1 1.008000 ! Nucleic acid amine proton
! MASS 92 HN2 1.008000 ! Nucleic acid ring nitrogen proton
! MASS 93 HN3 1.008000 ! Nucleic acid aromatic carbon proton
! MASS 94 HN4 1.008000 ! Nucleic acid phosphate hydroxyl proton
! MASS 95 HN5 1.008000 ! Nucleic acid ribose hydroxyl proton
! MASS 96 HN6 1.008000 ! Nucleic acid ribose aliphatic proton
! MASS 97 HN7 1.008000 ! Nucleic acid proton (equivalent to protein HA)
! MASS 98 HN8 1.008000 ! Bound to CN8 in nucleic acids/model compounds
! MASS 99 HN9 1.008000 ! Bound to CN9 in nucleic acids/model compounds
! MASS 100 CN1 12.011000 ! Nucleic acid carbonyl carbon
! MASS 101 CN1T 12.011000 ! Nucleic acid carbonyl carbon (T/U C2)
! MASS 102 CN2 12.011000 ! Nucleic acid aromatic carbon to amide
! MASS 103 CN3 12.011000 ! Nucleic acid aromatic carbon
! MASS 104 CN3T 12.011000 ! Nucleic acid aromatic carbon, Thy C5
! MASS 105 CN4 12.011000 ! Nucleic acid purine C8 and ADE C2
! MASS 106 CN5 12.011000 ! Nucleic acid purine C4 and C5
! MASS 107 CN5G 12.011000 ! Nucleic acid guanine C5
! MASS 108 CN7 12.011000 ! Nucleic acid carbon (equivalent to protein CT1)
! MASS 109 CN7B 12.011000 ! Nucleic acid aliphatic carbon for C1'
! MASS 110 CN8 12.011000 ! Nucleic acid carbon (equivalent to protein CT2)
! MASS 111 CN8B 12.011000 ! Nucleic acid carbon (equivalent to protein CT2)
! MASS 112 CN9 12.011000 ! Nucleic acid carbon (equivalent to protein CT3)
! MASS 113 NN1 14.007000 ! Nucleic acid amide nitrogen
! MASS 114 NN2 14.007000 ! Nucleic acid protonated ring nitrogen
! MASS 115 NN2B 14.007000 ! From NN2, for N9 in GUA different from ADE
! MASS 116 NN2U 14.007000 ! Nucleic acid protonated ring nitrogen, ura N3
! MASS 117 NN2G 14.007000 ! Nucleic acid protonated ring nitrogen, gua N1
! MASS 118 NN3 14.007000 ! Nucleic acid unprotonated ring nitrogen
! MASS 119 NN3A 14.007000 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
! MASS 120 NN3G 14.007000 ! Nucleic acid unprotonated ring nitrogen, gua N3
! MASS 121 NN4 14.007000 ! Nucleic acid purine N7
! MASS 122 NN6 14.007000 ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
! MASS 123 ON1 15.999400 ! Nucleic acid carbonyl oxygen
! MASS 124 ON1C 15.999400 ! Nucleic acid carbonyl oxygen, cyt O2
! MASS 125 ON2 15.999400 ! Nucleic acid phosphate ester oxygen
! MASS 126 ON3 15.999400 ! Nucleic acid =O in phosphate
! MASS 127 ON4 15.999400 ! Nucleic acid phosphate hydroxyl oxygen
! MASS 128 ON5 15.999400 ! Nucleic acid ribose hydroxyl oxygen
! MASS 129 ON6 15.999400 ! Nucleic acid deoxyribose ring oxygen
! MASS 130 ON6B 15.999400 ! Nucleic acid ribose ring oxygen
! MASS 131 P 30.974000 ! phosphorus
! MASS 132 P2 30.974000 ! phosphorus, adm, 2011 DNA update
!
! ! (Following lines from par_all36_prot.prm)
! MASS 31 H 1.00800 ! polar H
! MASS 32 HC 1.00800 ! N-ter H
! MASS 33 HA 1.00800 ! nonpolar H
! MASS 34 HP 1.00800 ! aromatic H
! MASS 35 HB1 1.00800 ! backbone H
! MASS 36 HB2 1.00800 ! aliphatic backbone H, to CT2
! MASS 37 HR1 1.00800 ! his he1, (+) his HG,HD2
! MASS 38 HR2 1.00800 ! (+) his HE1
! MASS 39 HR3 1.00800 ! neutral his HG, HD2
! MASS 40 HS 1.00800 ! thiol hydrogen
! MASS 41 HE1 1.00800 ! for alkene; RHC=CR
! MASS 42 HE2 1.00800 ! for alkene; H2C=CR
! MASS 43 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
! MASS 44 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
! MASS 45 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
! MASS 46 C 12.01100 ! carbonyl C, peptide backbone
! MASS 47 CA 12.01100 ! aromatic C
! MASS 48 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters
! MASS 49 CT1 12.01100 ! aliphatic sp3 C for CH
! MASS 50 CT2 12.01100 ! aliphatic sp3 C for CH2
! MASS 51 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu
! MASS 52 CT3 12.01100 ! aliphatic sp3 C for CH3
! MASS 53 CPH1 12.01100 ! his CG and CD2 carbons
! MASS 54 CPH2 12.01100 ! his CE1 carbon
! MASS 55 CPT 12.01100 ! trp C between rings
! MASS 56 CY 12.01100 ! TRP C in pyrrole ring
! MASS 57 CP1 12.01100 ! tetrahedral C (proline CA)
! MASS 58 CP2 12.01100 ! tetrahedral C (proline CB/CG)
! MASS 59 CP3 12.01100 ! tetrahedral C (proline CD)
! MASS 60 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2
! MASS 61 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1
! MASS 62 CS 12.01100 ! thiolate carbon
! MASS 63 CE1 12.01100 ! for alkene; RHC=CR
! MASS 64 CE2 12.01100 ! for alkene; H2C=CR
! MASS 65 CAI 12.01100 ! aromatic C next to CPT in trp
! MASS 66 N 14.00700 ! proline N
! MASS 67 NR1 14.00700 ! neutral his protonated ring nitrogen
! MASS 68 NR2 14.00700 ! neutral his unprotonated ring nitrogen
! MASS 69 NR3 14.00700 ! charged his ring nitrogen
! MASS 70 NH1 14.00700 ! peptide nitrogen
! MASS 71 NH2 14.00700 ! amide nitrogen
! MASS 72 NH3 14.00700 ! ammonium nitrogen
! MASS 73 NC2 14.00700 ! guanidinium nitrogen
! MASS 74 NY 14.00700 ! TRP N in pyrrole ring
! MASS 75 NP 14.00700 ! Proline ring NH2+ (N-terminal)
! MASS 76 O 15.99900 ! carbonyl oxygen
! MASS 77 OB 15.99900 ! carbonyl oxygen in acetic acid
! MASS 78 OC 15.99900 ! carboxylate oxygen
! MASS 79 OH1 15.99900 ! hydroxyl oxygen
! MASS 80 OS 15.99940 ! ester oxygen
! MASS 81 S 32.06000 ! sulphur
! MASS 82 SM 32.06000 ! sulfur C-S-S-C type
! MASS 83 SS 32.06000 ! thiolate sulfur
!
!
! ! (Following lines from par_all36_water_ions.prm)
! MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN
! MASS 2 HX 1.00800 ! hydroxide hydrogen
! MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN
! MASS 4 OX 15.99940 ! hydroxide oxygen
! MASS 5 LIT 6.94100 ! Lithium ion
! MASS 6 SOD 22.98977 ! Sodium Ion
! MASS 7 MG 24.30500 ! Magnesium Ion
! MASS 8 POT 39.09830 ! Potassium Ion
! MASS 9 CAL 40.08000 ! Calcium Ion
! MASS 10 RUB 85.46780 ! Rubidium Ion
! MASS 11 CES 132.90545 ! Cesium Ion
! MASS 12 BAR 137.32700 ! Barium Ion
! MASS 13 ZN 65.37000 ! zinc (II) cation
! MASS 14 CAD 112.41100 ! cadmium (II) cation
! MASS 15 CLA 35.45000 ! Chloride Ion
!
! The following flexible-parameters section was removed by combine-parameters.pl
! EQUI
BONDS
! (Following lines from par_all35_ethers.prm)
!! Alkane standard C27 parameeters. Not modified from original.
CC31A HCA1A 309.00 1.111 ! alkanes, 4/98
CC32A HCA2A 309.00 1.111 ! alkanes, 4/98
CC33A HCA3A 322.00 1.111 ! alkanes, 4/98
CC30A CC32A 222.50 1.538 ! 10/98
CC30A CC33A 222.50 1.538 ! 10/98
CC31A CC31A 222.50 1.500 ! alkanes, 3/92
CC31A CC32A 222.50 1.538 ! alkanes, 3/92
CC31A CC33A 222.50 1.538 ! alkanes, 3/92
CC32A CC32A 222.50 1.530 ! alkanes, 3/92
CC32A CC33A 222.50 1.528 ! alkanes, 3/92
CC33A CC33A 222.50 1.530 ! alkanes, 3/92
CC325A CC325A 195.00 1.548 ! cyclopentane CPEN 10/17/05 viv
CC325A HCA25A 307.00 1.116 ! cyclopentane CPEN 10/17/05 viv
CC325B OC305A 350.00 1.425 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv
CC325B CC325B 195.00 1.518 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv
CC325B HCA25A 307.00 1.100 ! THF, THF neutron diffr., 5/30/06, viv
CC325B CC33A 222.50 1.528 ! TF2M, viv
CC32A OC30A 360.00 1.415 ! DEET, diethylether, alex
CC33A OC30A 360.00 1.415 ! DEET, diethylether, alex
CC326A HCA2A 309.00 1.111 ! THP, viv
CC326A CC326A 222.50 1.530 ! THP, viv
CC326A OC30A 360.00 1.415 ! DEET, diethylether, viv
! ********* V(angle) = Ktheta(Theta - Theta0)**2
! (Following lines from par_all36_carb.prm)
!V(bond) = Kb(b - b0)**2
!Kb: kcal/mole/A**2
!b0: A
!
! atom types Kb b0
!
! aldose, ketose, new!!!!! adm, 11/08
OC2D3 CC2O3 700.00 1.215 ! ketone MP2/6-31g*, CSD geometry
CC2O3 CC331 330.00 1.500 ! ketone MP2/6-31g*, CSD geometry
CC2O3 CC312 330.00 1.500 ! ketone
CC2O3 CC322 330.00 1.500 ! ketone
OC2D4 CC2O4 700.00 1.215 ! acetaldehyde, adm
HCR1 CC2O4 330.00 1.110 ! acetaldehyde, adm
CC2O4 CC331 250.00 1.500 ! acetaldehyde, adm
CC2O4 CC312 250.00 1.500 ! acetaldehyde, adm
! monosaccharide CC
CC311 CC311 222.50 1.500 ! par22 CT1 CT1
CC312 CC312 222.50 1.485 ! adm 11/08, glycerol
CC3161 CC3163 222.50 1.500 ! par22 CT1 CT1
CC3161 CC3263 222.50 1.500 ! CC3161 CC3163 og xtal xylose
CC312 CC322 222.50 1.485 ! adm 11/08, glycerol
CC301 CC331 222.50 1.538 ! genff CG301 CG331
CC311 CC321 222.50 1.538 ! par22 CT2 CT1
CC311 CC331 222.50 1.538 ! par22 CT3 CT1
CC331 CC3163 222.50 1.538 ! par22 CT3 CT1 og xtal alfuco
CC3161 CC3161 222.50 1.480 ! sng qm and crystal analysis
CC3261 CC3161 222.50 1.480 ! from CC3161 CC3161
CC3161 CC3162 222.50 1.480 ! sng qm and crystal analysis
CC3261 CC3062 222.50 1.515 ! og xtal kemyac
CC321 CC3163 222.50 1.490 ! sng qm and crystal analysis
CC312 CC3163 222.50 1.490 ! from CC321 CC3163
CC301 CC2O2 200.00 1.522 ! par22 CT1 CC
CC311 CC2O2 200.00 1.522 ! par22 CT1 CC
CC3163 CC2O2 200.00 1.480 ! og xtal
CC3062 CC2O2 200.00 1.480 ! og xtal
CC2O1 CC331 250.00 1.520 ! og ipaa and xtal acglua11 agalam10 nacman10
! model compound CC
CC321 CC331 222.50 1.528 ! par22 CT3 CT2
CC321 CC321 222.50 1.530 ! par22 CT2 CT2
CC321C CC321C 222.50 1.530 ! par22 CT2 CT2
CC321C CC321D 222.50 1.530 ! par22 CT2 CT2
CC321C CC311C 222.50 1.538 ! par22 CT2 CT1
CC321 CC311C 222.50 1.490 ! from CC321 CC3163
CC321C CC311D 222.50 1.538 ! par22 CT2 CT1
CC321D CC311C 222.50 1.538 ! par22 CT2 CT1
CC321 CC2O2 200.00 1.522 ! par22 CT2 CC
! CO
! hydroxyls
CC3161 OC311 410.00 1.410 ! og crystal analysis
CC3162 OC311 428.00 1.400 ! og crystal analysis
CC3062 OC311 428.00 1.400 ! from CC3162 OC311
CC301 OC311 428.00 1.420 ! par22 OH1 CT1
CC311 OC311 428.00 1.420 ! par22 OH1 CT1
CC312 OC311 400.00 1.420 ! adm 11/08, glycerol
CC311 OC311M 428.00 1.420 ! par22 OH1 CT1
CC321 OC311 428.00 1.420 ! par22 OH1 CT2
CC321 OC311M 428.00 1.420 ! par22 OH1 CT2
CC331 OC311M 428.00 1.420 ! par22 OH1 CT3
CC322 OC311 400.00 1.420 ! adm 11/08, glycerol
! sp2
CC2O1 OC2D1 620.00 1.230 ! par22 O C
CC2O2 OC2D2 525.00 1.260 ! par22 OC CC
! ethers
CC301 OC301 360.00 1.415 ! par35 CC32A OC30A
CC311 OC301 360.00 1.415 ! par35 CC32A OC30A
CC321 OC301 360.00 1.415 ! par35 CC32A OC30A
CC331 OC301 360.00 1.415 ! par35 CC33A OC30A
CC311D OC301 360.00 1.395 ! og disac model compounds 2 and 3
CC3162 OC301 360.00 1.395 ! og disac model compounds 2 3 og/rmv crystals
CC3062 OC301 360.00 1.395 ! from CC3162 OC301
CC311D OC302 360.00 1.415 ! og disac model compounds 4 5 6
CC3162 OC302 360.00 1.415 ! og disac model comps 4 5 6 og/rmv crystals
CC311C OC301 360.00 1.435 ! og disac model compounds 7 8 9 and 10
CC3161 OC301 360.00 1.415 ! og/rmv disac crystals
! pyran ring ethers
CC321D OC3C61 360.00 1.415 ! par34 CC326A OC30A
CC311D OC3C61 360.00 1.415 ! par34 CC326A OC30A
CC3162 OC3C61 360.00 1.425 ! og crystal analysis
CC3062 OC3C61 360.00 1.425 ! from CC3162 OC3C61
CC321C OC3C61 360.00 1.415 ! par34 CC326A OC30A
CC311C OC3C61 360.00 1.415 ! par34 CC326A OC30A
CC3163 OC3C61 360.00 1.425 ! sng qm and crystal analysis
CC3263 OC3C61 360.00 1.425 ! CC3263 OC3C61 og xylose xtal ok
! CN
NC2D1 CC311 320.00 1.430 ! par22 NH1 CT1
NC2D1 CC3161 320.00 1.430 ! par22 NH1 CT1
NC2D1 CC331 320.00 1.430 ! par22 NH1 CT3
NC2D1 CC2O1 370.00 1.345 ! par22 NH1 C
! CH
CC311 HCA1 309.00 1.111 ! par22 HA CT1
CC312 HCA1 309.00 1.111 ! par22 HA CT1
CC3161 HCA1 309.00 1.111 ! par22 HA CT1
CC3162 HCA1 309.00 1.111 ! par22 HA CT1
CC3163 HCA1 309.00 1.111 ! par22 HA CT1
CC311C HCA1 309.00 1.111 ! par22 HA CT1
CC311D HCA1 309.00 1.111 ! par22 HA CT1
CC321 HCA2 309.00 1.111 ! par22 HA CT2
CC322 HCA2 309.00 1.111 ! par22 HA CT2
CC3263 HCA2 309.00 1.111 ! par22 HA CT2
CC331 HCA3 322.00 1.111 ! par22 HA CT3
CC321C HCA2 309.00 1.111 ! par22 HA CT2
CC321D HCA2 309.00 1.111 ! par22 HA CT2
CC3261 HCA2 309.00 1.111 ! par22 HA CT2
! OH
OC311 HCP1 545.00 0.960 ! par22 OH1 H
OC311M HCP1 545.00 0.960 ! par22 OH1 H
OC311M HCP1M 545.00 0.960 ! par22 OH1 H
! NH
NC2D1 HCP1 440.00 0.997 ! par22 NH1 H
! THF parameters for furanoses; viv, added by erh
CC322C OC3C5M 350.00 1.425 ! par34 CC325B OC305A
CC322C CC322C 195.00 1.518 ! par34 CC325B CC325B
CC322C HCA2C2 307.00 1.100 ! par34 CC325B HCA25A
! THF w/methyl for furanoses; viv,
! erh added and corrected for atom type, giving better pure solvent results 7/08
CC312C CC331 222.50 1.528 ! par34 CC325B CC33A
CC312C OC3C5M 350.00 1.425 ! par34 CC325B OC305A
CC312C CC322C 195.00 1.518 ! par34 CC325B CC325B
CC312C HCA1C2 307.00 1.100 ! par34 CC325B HCA25A
! OMe-THF param for omef patch
CC312C OC301 360.00 1.395 ! erh xtal analysis on disac
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! monosaccharide furanoses; erh modified 10/25/07!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! CO
OC3C51 CC3152 350.00 1.425 ! par34 CC325B OC305A
OC3C51 CC3051 350.00 1.425 ! par34 CC325B OC305A
OC3C51 CC3153 350.00 1.425 ! par34 CC325B OC305A
OC311 CC3152 428.00 1.395 ! erh crystal analysis on furanose 3/09
OC311 CC3051 428.00 1.395 ! erh crystal analysis on furanose 3/09
OC311 CC3151 410.00 1.395 ! erh crystal analysis on furanose 3/09
! CH
CC3152 HCA1 309.00 1.111 ! par22 HA CT1
CC3251 HCA2 307.00 1.100 ! par_carb CC322C HCA2C2
CC3151 HCA1 309.00 1.111 ! par22 HA CT1
CC3153 HCA1 309.00 1.111 ! par22 HA CT1
! CC
CC3152 CC3251 195.00 1.508 ! erh crystal analysis on furanose 3/09
CC3051 CC3251 195.00 1.508 ! erh crystal analysis on furanose 3/09
CC3251 CC3151 195.00 1.508 ! erh crystal analysis on furanose 3/09
CC3151 CC3153 195.00 1.508 ! erh crystal analysis on furanose 3/09
CC3151 CC3152 195.00 1.508 ! erh crystal analysis on furanose 3/09
CC3151 CC3051 195.00 1.508 ! erh crystal analysis on furanose 3/09
CC3151 CC3151 195.00 1.508 ! erh crystal analysis on furanose 3/09
CC3153 CC321 222.50 1.490 ! par_carb CC321 CC3163 (sng qm/crystal mod); erh 2/09
CC3051 CC321 222.50 1.490 ! par_carb CC321 CC3163 (sng qm/crystal mod); erh 2/09
! OMe-furanose param for fomea/b patch
CC3152 OC301 360.00 1.395 ! erh xtal analysis on disac
!*******************end of furanoses************************************
!Added by sai for modelling phosphate
CC321D CC311D 222.50 1.538 ! par22 CT2 CT1
CC311D CC311D 222.50 1.538 ! par22 CT2 CT1
CC3161 OC30P 360.00 1.425 !
CC311D OC30P 360.00 1.425 !
CC3162 OC30P 360.00 1.425 !
CC321 OC30P 360.00 1.452 !
OC30P PC 270.0 1.675 !
OC2DP PC 580.0 1.525 !
OC312 PC 237.0 1.61 !
OC312 HCP1 545.0 0.960 !
SC OC2DP 540.0 1.448 ! methylsulfate
SC OC30P 250.0 1.610 ! methylsulfate
!*******************end of phosphates***********************************
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! pyranose/furanose-furanose linkages, pram
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!model compounds
CC312D OC301 360.00 1.395 ! OMe-THF CC312C OC301
CC312D OC3C5M 350.00 1.425 ! OMe-THF CC312C OC3C5M
CC312D CC322C 195.00 1.518 ! THF w/me CC312C CC322C
CC312D HCA1 307.00 1.100 ! THF w/me CC312C HCA1C2
CC312D OC302 360.00 1.425 ! pram, modified (from OMe-THF) to match model comp 1(raman et al.) QM minima geometry and SUCROS04 crystal
CC312C HCA1 307.00 1.100 ! THF w/me CC312C HCA1C2
CC312C CC321 222.50 1.500 ! pram, modified 12/26/2010 (from THF w/me) to match model comp 2(raman et al.) QM minima geometry
CC331 OC303 360.00 1.415 ! Ome-THF CC331 OC301
CC312C OC303 360.00 1.425 ! pram, modified (from OMe-THF) to match model comp 3(raman et al.) QM minima geometry
CC311D OC303 360.00 1.395 ! CC311D OC301
!full sugars
CC3051 OC302 360.00 1.425 ! CC312D OC301 - model compound 1 (raman et. al.), crystal analysis
CC3162 OC303 360.00 1.395 ! CC311D OC303 - model compound 3 (raman et. al.)
OC303 CC3151 360.00 1.425 ! CC312C OC303 - model compound 3 (raman et. al.)
OC301 CC3051 360.00 1.395 ! CC312C OC301 - Ome-THF
!*******************end of pyranose-fruanose****************************
! Original TIP3P water parameters
!HCTIP3 HCTIP3 0.00 1.5139 ! TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
!OCTIP3 HCTIP3 450.00 0.9572 ! TIPS3P GEOMETRY
!****************** ANGLES ************
! (Following lines from par_all36_lipid.prm)
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
CTL3 CL 200.0 1.522 ! methyl acetate
CTL2 CL 200.0 1.522 ! methyl acetate
CTL1 CL 200.0 1.522 ! methyl acetate
CTL1 CCL 200.0 1.522 ! for POPS
OBL CL 750.0 1.220 ! methyl acetate
OCL CL 525.0 1.260 ! acetate, protein
OCL CCL 525.0 1.260 ! for POPS
OSL CL 150.0 1.334 ! methyl acetate
OSLP CL 150.0 1.334 ! methyl acetate
OHL CL 230.0 1.40 ! methyl acetate
HOL OHL 545.0 0.960 ! acetic acid
CTL1 HAL1 309.00 1.111 ! alkanes, 3/92
CTL1 HBL 330.00 1.080 ! for POPS
CTL2 HAL2 309.00 1.111 ! alkanes, 4/98
CTL3 HAL3 322.00 1.111 ! alkanes, 4/98
CTL3 OSL 340.0 1.43 ! phosphate
CTL2 OSL 340.0 1.43 ! phosphate
CTL1 OSL 340.0 1.43 ! phosphate
CTL3 OSLP 340.0 1.43 !
CTL2 OSLP 340.0 1.43 !
CTL1 OSLP 340.0 1.43 !
OSL PL 270.0 1.60 ! phosphate
OSLP PL 270.0 1.60 !
O2L PL 580.0 1.48 ! phosphate
OHL PL 237.0 1.59 ! phosphate
NH3L HCL 410.0 1.04 ! ethanolamine
NH3L CTL1 200.0 1.48 ! for POPS
NH3L CTL2 261.0 1.51 ! ethanolamine
NTL CTL2 215.00 1.51 ! tetramethylammonium
NTL CTL5 215.00 1.51 ! tetramethylammonium
CTL5 HL 300.00 1.08 ! tetramethylammonium
CTL2 HL 300.00 1.08 ! tetramethylammonium
CTL1 CTL1 222.500 1.500 ! alkanes, 3/92
CTL1 CTL2 222.500 1.538 ! alkanes, 3/92
CTL1 CTL3 222.500 1.538 ! alkanes, 3/92
CTL2 CTL2 222.500 1.530 ! alkanes, 3/92
CTL2 CTL3 222.500 1.528 ! alkanes, 3/92
CTL3 CTL3 222.500 1.530 ! alkanes, 3/92
OHL CTL1 428.0 1.420 ! glycerol
OHL CTL2 428.0 1.420 ! glycerol
OHL CTL3 428.0 1.420 ! glycerol
SL O2L 540.0 1.448 ! methylsulfate
SL OSL 250.0 1.575 ! methylsulfate
CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95
HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95
CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95
CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95
HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95
CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95
CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95
! (Following lines from par_all36_na.prm)
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
!2-(aminobutyl)-1,3-propandiol terms
CN8 NN6 200.000 1.480 ! methylammonium
NN6 HN1 403.000 1.040 ! methylammonium
!abasic deoxynucleoside
ON6 CN8B 260.0 1.420 ! susil
CN8 CN8B 222.50 1.528 ! Alkanes, sacred
!
CN1 CN3 302.0 1.409 !U, adm jr. 11/97
CN1 CN3T 302.0 1.403 !T, adm jr. 11/97
CN1 CN5G 302.0 1.360 !G, adm jr. 11/97
CN1 NN2 380.0 1.367 !C, adm jr. 11/97
CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97
CN1 NN2G 340.0 1.396 !G, adm jr. 11/97
CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97
CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97
CN1 NN3 350.0 1.335 !C, adm jr. 11/97
CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91
CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91
CN2 CN3 320.0 1.406 !C, adm jr. 11/97
CN2 CN5 360.0 1.358 !A, adm jr. 11/97
CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91
CN2 NN2G 400.0 1.392 !G
CN2 NN3 450.0 1.343 !C
CN2 NN3A 400.0 1.342 !A, adm jr. 11/97
CN2 NN3G 320.0 1.326 !G, adm jr. 11/97
CN3 CN3 500.0 1.326 !C,U adm jr. 11/97
CN3 CN3T 560.0 1.320 !T, adm jr. 11/97
CN3T CN9 230.0 1.478 !T, adm jr. 11/97
CN3 HN3 350.0 1.09 !C,U, JWK
CN3T HN3 350.0 1.09 !T, JWK
CN3 NN2 302.0 1.343 !C, adm jr. 11/97
CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97
CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91
CN4 NN2 320.0 1.374 !A, adm jr. 11/97
CN4 NN2B 300.0 1.378 !G, adm jr. 11/97
CN4 NN3A 420.0 1.322 !A, adm jr. 11/97
CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97
CN5 CN5 310.0 1.361 !A, adm jr. 11/97
CN5 CN5G 320.0 1.350 !G, adm jr. 11/97
CN5 NN2 300.0 1.375 !A, adm jr. 11/97
CN5 NN2B 302.0 1.375 !G, adm jr. 11/97
CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91
CN5 NN3G 350.0 1.315 !G, adm jr. 11/97
CN5 NN4 310.0 1.355 !A, adm jr. 11/97
CN5G NN4 310.0 1.365 !G, adm jr. 11/97
CN8 CN8 222.50 1.528 !Alkanes, sacred
CN8 CN9 222.50 1.528 !Alkanes, sacred
CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR.
CN8 ON5 428.0 1.42 !RIBOSE, MeOH
CN9 HN9 322.0 1.111 !alkanes
CN9 ON2 340.0 1.43 !DMP, ADM Jr.
HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91
HN2 NN2 474.0 1.01 !C,U, JWK
HN2 NN2B 474.0 1.01 !G, adm jr. 11/97
HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91
HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91
HN4 ON4 545.0 0.960 !MP_1, ADM Jr.
ON2 P 270.0 1.60 !DMP, ADM Jr.
ON2 P2 270.0 1.60 !DMP, ADM Jr., adm, 2011 DNA update
ON3 P 580.0 1.48 !DMP, ADM Jr.
ON3 P2 580.0 1.48 !DMP, ADM Jr., adm, 2011 DNA update
ON4 P 237.0 1.58 !MP_1, ADM Jr.
ON4 P2 237.0 1.58 !MP_1, ADM Jr., adm, 2011 DNA update
!NN5 HN1 460.0 1.01 !sugar model, adm jr.
!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
CN7B ON6 260.0 1.420 ! From exp
CN7B CN8 200.0 1.518 ! From exp
CN7 ON6 240.0 1.446 ! Fom exp.
CN7 CN7 222.5 1.529 ! From exp
CN7 CN8 222.5 1.516 ! From exp.
CN7 CN9 222.5 1.516 ! for 5MET, From alkanes
CN7 HN7 309.0 1.111 !Alkanes, sacred
CN8 HN8 309.0 1.111 !Alkanes, sacred
CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF)
!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
CN7B ON6B 260.0 1.420 ! From CN7B ON6
CN7 ON6B 240.0 1.480 ! From CN7 ON6
CN7B CN7B 200.0 1.450 !
CN7 CN7B 222.5 1.460 ! Specific to RNA
!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
CN7 CN8B 222.5 1.512 ! From exp.
CN8B ON2 320.0 1.44 ! From exp
!CN8B ON5 250.0 1.44 ! From CN8B ON2
CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
CN7 ON2 310.0 1.433 ! From exp
CN7B ON2 310.0 1.433 ! From exp, for NADPH and bkbmod
!CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO
CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
! C1'-N9 (purines)/C1'-N1 (pyrimidines)
CN9 NN2 400.0 1.456 !9-M-A/C, adm jr.
CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
CN7B NN2 220.0 1.456 !A/C
CN7B NN2B 220.0 1.458 !G/T/U
! C5'-H in model compounds and DNA
CN8B HN8 309.0 1.111 !Alkanes, sacred
ON5 HN5 545.0 0.960 !RIBOSE, MeOH
!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
!CN7B ON5 250.0 1.400 ! From CN7 ON5
CN7B ON5 428.0 1.400 ! check adm jr.,
!FC should be 428.000 based on Meoh
!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@
!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
CN8 ON2 340.0 1.44 !
!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@
! (Following lines from par_all36_prot.prm)
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
NH2 CT1 240.000 1.4550 ! From LSN NH2-CT2
!
!Indole/Tryptophan
CA CAI 305.000 1.3750 ! from CA CA
CAI CAI 305.000 1.3750 ! atm, methylindole, fit CCDSS
CPT CA 300.000 1.3600 ! atm, methylindole, fit CCDSS
CPT CAI 300.000 1.3600 ! atm, methylindole, fit CCDSS
CPT CPT 360.000 1.3850 ! atm, methylindole, fit CCDSS
CY CA 350.000 1.3650 ! trj, adm jr., 5/08/91, indole CCDB structure search
CY CAI 350.000 1.3650 ! from CY CA
CY CPT 350.000 1.4300 ! atm, methylindole, fit CDS data
CY CT3 375.000 1.4920 ! atm, methylindole, fit CDS data
CY CT2 375.000 1.4920 ! atm, methylindole, fit CDS data
HP CAI 340.000 1.0800 ! from HP CA
HP CY 350.000 1.0800 ! trp, adm jr., 12/30/91
NY CA 270.000 1.3700 ! trp, adm jr., 12/30/91
NY CPT 270.000 1.3700 ! atm, methylindole, from CCDS 1/17/04
NY H 537.500 0.9760 ! atm, methylindole, 1/17/04
CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA1 CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA2 CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA1 CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA2 CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92