* AMBER parm99 force field conversion * See: J Comp. Chem. (2000) 21, 1049-1074. * ! ! This is a hand-conversion of the parm99 force field ! parm99.dat file. All the atom type names are the same except where ! otherwise noted. ! ! note: types N* remaned to NS ! C* renamed to CS ! ! note: the HO and HW nonbonded parameters, although zero in ! Cornell et al. should not have a 0.0 vdw radius in CHARMM ! to avoid difficulties with the 0.0/0.0 in the FAST OFF ! van der Waal code... ! ! note: the default nonbonded options chosen here are to match AMBER. ! It is not recommended that users actually run with GROUP based ! truncation and a switch unless really trying to match AMBER. ! Better would be ATOM based FSHIFT VSHIFT, however note that this ! does modify the energies (and effectively the parameters). ! ! Also note that long-range interactions are handeled differently between ! AMBER and CHARMM. To avoid differences when comparing energies and ! forces the the cuttoffs were set to be large in the individule ! comparison input files, i.e. 80 Angs. ! ! created by Jeffery Klauda (jbklauda@umd.edu) ! BONDS OW HW 553.0 0.9572 ! TIP3P water HW HW 553.0 1.5136 ! TIP3P water C C 310.0 1.525 ! Junmei et al, 1999 C CA 469.0 1.409 ! JCC,7,(1986),230; (not used any more in TYR) C CB 447.0 1.419 ! JCC,7,(1986),230; GUA C CM 410.0 1.444 ! JCC,7,(1986),230; THY,URA C CT 317.0 1.522 ! JCC,7,(1986),230; AA C N 490.0 1.335 ! JCC,7,(1986),230; AA C NS 424.0 1.383 ! JCC,7,(1986),230; CYT,URA C NA 418.0 1.388 ! JCC,7,(1986),230; GUA.URA C NC 457.0 1.358 ! JCC,7,(1986),230; CYT C O 570.0 1.229 ! JCC,7,(1986),230; AA,CYT,GUA,THY,URA C O2 656.0 1.250 ! JCC,7,(1986),230; GLU,ASP C OH 450.0 1.364 ! JCC,7,(1986),230; (not used any more for TYR) C OS 450.0 1.323 ! Junmei et al, 1999 C H4 367.0 1.080 ! Junmei et al, 1999 C H5 367.0 1.080 ! Junmei et al, 1999 CA CA 469.0 1.400 ! JCC,7,(1986),230; BENZENE,PHE,TRP,TYR CA CB 469.0 1.404 ! JCC,7,(1986),230; ADE,TRP CA CM 427.0 1.433 ! JCC,7,(1986),230; CYT CA CN 469.0 1.400 ! JCC,7,(1986),230; TRP CA CT 317.0 1.510 ! JCC,7,(1986),230; PHE,TYR CA HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR CA H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; no assigned CA N2 481.0 1.340 ! JCC,7,(1986),230; ARG,CYT,GUA CA NA 427.0 1.381 ! JCC,7,(1986),230; GUA CA NC 483.0 1.339 ! JCC,7,(1986),230; ADE,CYT,GUA CA OH 450.0 1.364 ! substituted for C-OH in tyr CB CB 520.0 1.370 ! JCC,7,(1986),230; ADE,GUA CB NS 436.0 1.374 ! JCC,7,(1986),230; ADE,GUA CB NB 414.0 1.391 ! JCC,7,(1986),230; ADE,GUA CB NC 461.0 1.354 ! JCC,7,(1986),230; ADE,GUA CD HA 367.0 1.080 ! Junmei et al, 1999 CD CD 469.0 1.400 ! Junmei et al, 1999 CD CM 549.0 1.350 ! Junmei et al, 1999 CD CT 317.0 1.510 ! Junmei et al, 1999 CK H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA CK NS 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA CK NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA CM CM 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA CM CT 317.0 1.510 ! JCC,7,(1986),230; THY CM HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA CM H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA CM H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; not assigned CM NS 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA CM OS 480.0 1.240 ! Junmei et al, 1999 CQ H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE CQ NC 502.0 1.324 ! JCC,7,(1986),230; ADE CT CT 310.0 1.526 ! JCC,7,(1986),230; AA, SUGARS CT HC 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, SUGARS CT H1 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE CT H2 340.0 1.090 ! changed from 331 bsd on NMA nmodes; SUGARS CT H3 340.0 1.090 ! changed from 331 bsd on NMA nmodes; not assigned CT HP 340.0 1.090 ! changed from 331; AA-lysine, methyl ammonium cation CT NS 337.0 1.475 ! JCC,7,(1986),230; ADE,CYT,GUA,THY,URA CT N2 337.0 1.463 ! JCC,7,(1986),230; ARG CT OH 320.0 1.410 ! JCC,7,(1986),230; SUGARS CT OS 320.0 1.410 ! JCC,7,(1986),230; NUCLEIC ACIDS CS HC 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes, not needed AA CS CB 388.0 1.459 ! JCC,7,(1986),230; TRP CS CT 317.0 1.495 ! JCC,7,(1986),230; TRP CS CW 546.0 1.352 ! JCC,7,(1986),230; TRP CB CN 447.0 1.419 ! JCC,7,(1986),230; TRP CC CT 317.0 1.504 ! JCC,7,(1986),230; HIS CC CV 512.0 1.375 ! JCC,7,(1986),230; HIS(delta) CC CW 518.0 1.371 ! JCC,7,(1986),230; HIS(epsilon) CC NA 422.0 1.385 ! JCC,7,(1986),230; HIS CC NB 410.0 1.394 ! JCC,7,(1986),230; HIS CN NA 428.0 1.380 ! JCC,7,(1986),230; TRP CR H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS CR NA 477.0 1.343 ! JCC,7,(1986),230; HIS CR NB 488.0 1.335 ! JCC,7,(1986),230; HIS CT N 337.0 1.449 ! JCC,7,(1986),230; AA CT N3 367.0 1.471 ! JCC,7,(1986),230; LYS CT NT 367.0 1.471 ! for neutral amines CT S 227.0 1.810 ! changed from 222.0 based on dimethylS nmodes CT SH 237.0 1.810 ! changed from 222.0 based on methanethiol nmodes CT CY 400.0 1.458 ! Howard et al JCC.16,243,1995 CT CZ 400.0 1.459 ! Howard et al JCC,16,243,1995 CV H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; HIS CV NB 410.0 1.394 ! JCC,7,(1986),230; HIS CW H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) CW NA 427.0 1.381 ! JCC,7,(1986),230; HIS,TRP CY NY 600.0 1.150 ! Howard et al JCC,16,243,1995 CZ CZ 600.0 1.206 ! Howard et al JCC,16,243,1995 CZ HZ 400.0 1.056 ! Howard et al JCC,16,243,1995 O2 P 525.0 1.480 ! JCC,7,(1986),230; NA PHOSPHATES OH P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES OS P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES H N2 434.0 1.010 ! JCC,7,(1986),230; ADE,CYT,GUA,ARG H NS 434.0 1.010 ! for plain unmethylated bases ADE,CYT,GUA,ARG H NA 434.0 1.010 ! JCC,7,(1986),230; GUA,URA,HIS H N 434.0 1.010 ! JCC,7,(1986),230; AA H N3 434.0 1.010 ! JCC,7,(1986),230; LYS H NT 434.0 1.010 ! for neutral amines HO OH 553.0 0.960 ! JCC,7,(1986),230; SUGARS,SER,TYR HO OS 553.0 0.960 ! JCC,7,(1986),230; NUCLEOTIDE ENDS HS SH 274.0 1.336 ! JCC,7,(1986),230; CYS S S 166.0 2.038 ! JCC,7,(1986),230; CYX (SCHERAGA) F CT 367.0 1.380 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 Cl CT 232.0 1.766 ! 6-31g* opt Br CT 159.0 1.944 ! Junmei et al,99 I CT 148.0 2.166 ! Junmei et al,99 F CA 386.0 1.359 ! Junmei et al,99 Cl CA 193.0 1.727 ! Junmei et al,99 I CA 171.0 2.075 ! Junmei et al,99 Br CA 172.0 1.890 ! Junmei et al,99 LP O 600.0 0.200 ! or 0.35 LP OH 600.0 0.200 ! or 0.35 LP OS 600.0 0.200 ! or 0.35 LP N3 600.0 0.200 ! or 0.35 LP NT 600.0 0.200 ! or 0.35 LP NB 600.0 0.200 ! or 0.35 histidines, nucleic acids LP NC 600.0 0.200 ! or 0.35 nucleic acids LP S 600.0 0.700 ! cys,cyx,met LP SH 600.0 0.700 ! cys,cyx ! BS0 Parameters with CI Perez et al. BJ 92: 3817 (2007) CI H1 340.0 1.090 ! CI CT 310.0 1.526 ! OS CI 320.0 1.410 ! OH CI 320.0 1.410 ! ! Added by Wei c3 os 301.5 1.439 ! From GAFF c3 c3 303.1 1.535 ! From GAFF c3 h1 335.9 1.093 ! From GAFF c3 na 334.7 1.456 ! From GAFF c3 h2 326.4 1.100 ! From GAFF ca nd 492.9 1.336 ! From GAFF cc nd 494.6 1.335 ! From GAFF cc h5 356.0 1.079 ! From GAFF ca nb 483.1 1.342 ! From GAFF ca h5 347.2 1.085 ! From GAFF ca nh 449.0 1.364 ! From GAFF hn nh 401.2 1.014 ! From GAFF c3 oh 314.1 1.426 ! From GAFF c3 n4 293.6 1.499 ! From GAFF hn n4 369.0 1.033 ! From GAFF c3 hx 338.7 1.091 ! From GAFF c3 hc 337.3 1.092 ! From GAFF c3 s4 233.8 1.807 ! From GAFF c c3 328.3 1.508 ! From GAFF THETAS HW OW HW 100. 104.52 ! TIP3P water HW HW OW 0. 127.74 ! (found in crystallographic water with 3 bonds) C C O 80.0 120.00 ! Junmei et al, 1999 acrolein C C OH 80.0 120.00 ! Junmei et al, 1999 CA C CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA CA C OH 70.0 120.00 ! AA (not used in tyr) CB C NA 70.0 111.30 ! NA CB C O 80.0 128.80 ! CM C NA 70.0 114.10 ! CM C O 80.0 125.30 ! CT C O 80.0 120.40 ! CT C O2 70.0 117.00 ! CT C N 70.0 116.60 ! AA general CT C CT 63.0 117.00 ! Junmei et al, 1999 CT C OS 80.0 115.00 ! Junmei et al, 1999 CT C OH 80.0 110.00 ! Junmei et al, 1999 NS C NA 70.0 115.40 ! NS C NC 70.0 118.60 ! NS C O 80.0 120.90 ! NA C O 80.0 120.60 ! NC C O 80.0 122.50 ! N C O 80.0 122.90 ! AA general O C O 80.0 126.00 ! AA COO- terminal residues O C OH 80.0 120.00 ! (check with Junmei for: theta0:120.0?) O C OS 80.0 125.00 ! Junmei et al, 1999 O2 C O2 80.0 126.00 ! AA GLU (SCH JPC 79,2379) H4 C C 50.0 120.00 ! Junmei et al, 1999 H4 C CM 50.0 115.00 ! Junmei et al, 1999 H4 C CT 50.0 115.00 ! Junmei et al, 1999 H4 C O 50.0 120.00 ! Junmei et al, 1999 H4 C OH 50.0 120.00 ! Junmei et al, 1999 H5 C N 50.0 120.00 ! Junmei et al, 1999 H5 C O 50.0 119.00 ! Junmei et al, 1999 H5 C OH 50.0 107.00 ! Junmei et al, 1999 H5 C OS 50.0 107.00 ! Junmei et al, 1999 C CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes C CA HA 50.0 120.00 ! AA (not used in tyr) CA CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes CA CA CB 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes CA CA CT 70.0 120.00 ! CA CA HA 50.0 120.00 ! CA CA H4 50.0 120.00 ! CA CA OH 70.0 120.00 ! replacement in tyr CA CA CN 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA trp CB CA HA 50.0 120.00 ! CB CA H4 50.0 120.00 ! CB CA N2 70.0 123.50 ! CB CA NC 70.0 117.30 ! CM CA N2 70.0 120.10 ! CM CA NC 70.0 121.50 ! CN CA HA 50.0 120.00 ! AA trp NA CA NC 70.0 123.30 ! N2 CA NA 70.0 116.00 ! N2 CA NC 70.0 119.30 ! N2 CA N2 70.0 120.00 ! AA arg F CA CA 70.0 121.00 ! Junmei et al,99 Cl CA CA 70.0 118.80 ! Junmei et al,99 Br CA CA 70.0 118.80 ! Junmei et al,99 I CA CA 70.0 118.80 ! Junmei et al,99 C CB CB 63.0 119.20 ! changed from 85.0 bsd on C6H6 nmodes; NA gua C CB NB 70.0 130.00 ! CA CB CB 63.0 117.30 ! changed from 85.0 bsd on C6H6 nmodes; NA ade CA CB NB 70.0 132.40 ! CB CB NS 70.0 106.20 ! CB CB NB 70.0 110.40 ! CB CB NC 70.0 127.70 ! CS CB CA 63.0 134.90 ! changed from 85.0 bsd on C6H6 nmodes; AA trp CS CB CN 63.0 108.80 ! changed from 85.0 bsd on C6H6 nmodes; AA trp CA CB CN 63.0 116.20 ! changed from 85.0 bsd on C6H6 nmodes; AA trp NS CB NC 70.0 126.20 ! CD CD CM 63.0 120.00 ! Junmei et al, 1999 CD CD CT 70.0 120.00 ! Junmei et al, 1999 CM CD CT 70.0 120.00 ! Junmei et al, 1999 HA CD HA 35.0 119.00 ! Junmei et al, 1999 HA CD CD 50.0 120.00 ! Junmei et al, 1999 HA CD CM 50.0 120.00 ! Junmei et al, 1999 H5 CK NS 50.0 123.05 ! H5 CK NB 50.0 123.05 ! NS CK NB 70.0 113.90 ! C CM CM 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy C CM CT 70.0 119.70 ! C CM HA 50.0 119.70 ! C CM H4 50.0 119.70 ! CA CM CM 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt CA CM HA 50.0 123.30 ! CA CM H4 50.0 123.30 ! CM CM CT 70.0 119.70 ! CM CM HA 50.0 119.70 ! CM CM H4 50.0 119.70 ! CM CM NS 70.0 121.20 ! CM CM OS 80.0 125.00 ! Junmei et al, 1999 H4 CM NS 50.0 119.10 ! H4 CM OS 50.0 113.00 ! Junmei et al, 1999 HA CM HA 35.0 120.00 ! Junmei et al, 1999 HA CM CD 50.0 120.00 ! Junmei et al, 1999 HA CM CT 50.0 120.00 ! Junmei et al, 1999 NC CQ NC 70.0 129.10 ! H5 CQ NC 50.0 115.45 ! H1 CT H1 35.0 109.50 ! H1 CT NS 50.0 109.50 ! changed based on NMA nmodes H1 CT OH 50.0 109.50 ! changed based on NMA nmodes H1 CT OS 50.0 109.50 ! changed based on NMA nmodes H1 CT CM 50.0 109.50 ! Junmei et al, 1999 H1 CT CY 50.0 110.00 ! Junmei et al, 1999 H1 CT CZ 50.0 110.00 ! Junmei et al, 1999 H1 CT N 50.0 109.50 ! AA general changed based on NMA nmodes H1 CT S 50.0 109.50 ! AA cys changed based on NMA nmodes H1 CT SH 50.0 109.50 ! AA cyx changed based on NMA nmodes H1 CT N2 50.0 109.50 ! AA arg changed based on NMA nmodes H1 CT NT 50.0 109.50 ! neutral amines H2 CT H2 35.0 109.50 ! AA lys H2 CT NS 50.0 109.50 ! changed based on NMA nmodes H2 CT OS 50.0 109.50 ! changed based on NMA nmodes HP CT HP 35.0 109.50 ! AA lys, ch3nh4+ HP CT N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes HC CT HC 35.0 109.50 ! HC CT CM 50.0 109.50 ! changed based on NMA nmodes HC CT CD 50.0 109.50 ! Junmei et al, 1999 HC CT CZ 50.0 110.00 ! Junmei et al, 1999 C CT H1 50.0 109.50 ! AA general changed based on NMA nmodes C CT HP 50.0 109.50 ! AA zwitterion changed based on NMA nmodes C CT HC 50.0 109.50 ! AA gln changed based on NMA nmodes C CT N 63.0 110.10 ! AA general C CT N3 80.0 111.20 ! AA amino terminal residues C CT CT 63.0 111.10 ! AA general C CT OS 60.0 109.50 ! Junmei et al, 1999 CA CT HC 50.0 109.50 ! AA tyr changed based on NMA nmodes CC CT CT 63.0 113.10 ! AA his CC CT HC 50.0 109.50 ! AA his changed based on NMA nmodes CM CT CT 63.0 111.00 ! Junmei et al, 1999 (last change: Mar24,99) CM CT OS 50.0 109.50 ! Junmei et al, 1999 CT CT CT 40.0 109.50 ! CT CT HC 50.0 109.50 ! changed based on NMA nmodes CT CT H1 50.0 109.50 ! changed based on NMA nmodes CT CT H2 50.0 109.50 ! changed based on NMA nmodes CT CT HP 50.0 109.50 ! changed based on NMA nmodes CT CT NS 50.0 109.50 ! CT CT OH 50.0 109.50 ! CT CT OS 50.0 109.50 ! CT CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428) CT CT SH 50.0 108.60 ! AA cys CT CT CA 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379) CT CT N2 80.0 111.20 ! AA arg (JCP 76, 1439) CT CT N 80.0 109.70 ! AA ala, general (JACS 94, 2657) CT CT N3 80.0 111.20 ! AA lys (JCP 76, 1439) CT CT NT 80.0 111.20 ! neutral amines CT CT CY 63.0 110.00 ! Junmei et al, 1999 CT CT CZ 63.0 110.00 ! Junmei et al, 1999 CS CT CT 63.0 115.60 ! AA trp CS CT HC 50.0 109.50 ! AA trp changed based on NMA nmodes OS CT OS 160.0 101.00 ! Junmei et al, 1999 OS CT CY 50.0 110.00 ! Junmei et al, 1999 OS CT CZ 50.0 110.00 ! Junmei et al, 1999 OS CT NS 50.0 109.50 ! F CT F 77.0 109.10 ! JCC,13,(1992),963; F CT H1 50.0 109.50 ! JCC,13,(1992),963; F CT CT 50.0 109.00 ! F CT H2 50.0 109.50 ! Cl CT CT 50.0 108.50 ! (6-31g* opt value) Cl CT H1 50.0 108.50 ! (6-31g* opt value) Br CT CT 50.0 108.00 ! Junmei et al 99 Br CT H1 50.0 106.50 ! Junmei et al 99 I CT CT 50.0 106.00 ! Junmei et al,99 CT CC NA 70.0 120.00 ! AA his CT CC CV 70.0 120.00 ! AA his CT CC NB 70.0 120.00 ! AA his CV CC NA 70.0 120.00 ! AA his CW CC NA 70.0 120.00 ! AA his CW CC NB 70.0 120.00 ! AA his CT CC CW 70.0 120.00 ! AA his H5 CR NA 50.0 120.00 ! AA his H5 CR NB 50.0 120.00 ! AA his NA CR NA 70.0 120.00 ! AA his NA CR NB 70.0 120.00 ! AA his CC CV H4 50.0 120.00 ! AA his CC CV NB 70.0 120.00 ! AA his H4 CV NB 50.0 120.00 ! AA his CC CW H4 50.0 120.00 ! AA his CC CW NA 70.0 120.00 ! AA his CS CW H4 50.0 120.00 ! AA trp CS CW NA 70.0 108.70 ! AA trp H4 CW NA 50.0 120.00 ! AA his CB CS CT 70.0 128.60 ! AA trp CB CS CW 63.0 106.40 ! changed from 85.0 bsd on C6H6 nmodes; AA trp CT CS CW 70.0 125.00 ! AA trp CA CN CB 63.0 122.70 ! changed from 85.0 bsd on C6H6 nmodes; AA trp CA CN NA 70.0 132.80 ! AA trp CB CN NA 70.0 104.40 ! AA trp CT CY NY 80.0 180.00 ! Junmei et al, 1999 CT CZ CZ 80.0 180.00 ! Junmei et al, 1999 CZ CZ HZ 50.0 180.00 ! Junmei et al, 1999 C N CT 50.0 121.90 ! AA general C N H 50.0 120.00 ! AA general, gln, asn,changed based on NMA nmodes CT N H 50.0 118.04 ! AA general, changed based on NMA nmodes CT N CT 50.0 118.00 ! AA pro (DETAR JACS 99,1232) H N H 35.0 120.00 ! ade,cyt,gua,gln,asn ** C NS CM 70.0 121.60 ! C NS CT 70.0 117.60 ! C NS H 50.0 119.20 ! changed based on NMA nmodes CB NS CK 70.0 105.40 ! CB NS CT 70.0 125.80 ! CB NS H 50.0 125.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes CK NS CT 70.0 128.80 ! CK NS H 50.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes CM NS CT 70.0 121.20 ! CM NS H 50.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes CA N2 H 50.0 120.00 ! CA N2 CT 50.0 123.20 ! AA arg CT N2 H 50.0 118.40 ! AA arg H N2 H 35.0 120.00 ! CT N3 H 50.0 109.50 ! AA lys, changed based on NMA nmodes CT N3 CT 50.0 109.50 ! AA pro/nt H N3 H 35.0 109.50 ! AA lys, AA(end) CT NT H 50.0 109.50 ! neutral amines CT NT CT 50.0 109.50 ! neutral amines H NT H 35.0 109.50 ! neutral amines C NA C 70.0 126.40 ! C NA CA 70.0 125.20 ! C NA H 50.0 116.80 ! changed based on NMA nmodes CA NA H 50.0 118.00 ! changed based on NMA nmodes CC NA CR 70.0 120.00 ! AA his CC NA H 50.0 120.00 ! AA his, changed based on NMA nmodes CR NA CW 70.0 120.00 ! AA his CR NA H 50.0 120.00 ! AA his, changed based on NMA nmodes CW NA H 50.0 120.00 ! AA his, changed based on NMA nmodes CN NA CW 70.0 111.60 ! AA trp CN NA H 50.0 123.10 ! AA trp, changed based on NMA nmodes CB NB CK 70.0 103.80 ! CC NB CR 70.0 117.00 ! AA his CR NB CV 70.0 117.00 ! AA his C NC CA 70.0 120.50 ! CA NC CB 70.0 112.20 ! CA NC CQ 70.0 118.60 ! CB NC CQ 70.0 111.00 ! C OH HO 50.0 113.00 ! (not used in tyr anymore) CA OH HO 50.0 113.00 ! replacement in tyr CT OH HO 55.0 108.50 ! HO OH P 45.0 108.50 ! C OS CT 60.0 117.00 ! Junmei et al, 1999 CM OS CT 60.0 117.00 ! Junmei et al, 1999 CT OS CT 60.0 109.50 ! CT OS P 100.0 120.50 ! P OS P 100.0 120.50 ! O2 P OH 45.0 108.23 ! O2 P O2 140.0 119.90 ! O2 P OS 100.0 108.23 ! OH P OS 45.0 102.60 ! OS P OS 45.0 102.60 ! CT S CT 62.0 98.90 ! AA met CT S S 68.0 103.70 ! AA cyx (SCHERAGA JPC 79,1428) CT SH HS 43.0 96.00 ! changed from 44.0 based on methanethiol nmodes HS SH HS 35.0 92.07 ! AA cys CB NB LP 150.0 126.0 ! NA CC NB LP 150.0 126.0 ! his,NA CK NB LP 150.0 126.0 ! NA CR NB LP 150.0 126.0 ! his,NA CV NB LP 150.0 126.0 ! his,NA C NC LP 150.0 120.0 ! NA CA NC LP 150.0 120.0 ! NA CB NC LP 150.0 120.0 ! NA CQ NC LP 150.0 120.0 ! NA CT N3 LP 150.0 109.5 ! in neutral lysine H N3 LP 150.0 109.5 ! in neutral lysine CT NT LP 150.0 109.5 ! H NT LP 150.0 109.5 ! C O LP 150.0 120.0 ! LP O LP 150.0 120.0 ! C OH LP 150.0 120.0 ! CT OH LP 150.0 109.5 ! HO OH LP 150.0 109.5 ! LP OH LP 150.0 109.5 ! C OS LP 150.0 109.5 ! CM OS LP 150.0 109.5 ! methyl vinyl ether CT OS LP 150.0 109.5 ! LP OS LP 150.0 109.5 ! CT S LP 150.0 90.0 ! cys,cyx,met CT SH LP 150.0 90.0 ! cys,cyx,met P OS LP 150.0 109.5 ! NA LP S LP 150.0 180.0 ! cys,cyx,met LP SH LP 150.0 180.0 ! cys,cyx,met HS SH LP 150.0 90.0 ! cys ! BS0 Parameters with CI Perez et al. BJ 92: 3817 (2007) H1 CI CT 50.0 109.50 ! H1 CI H1 35.0 109.50 ! CI CT H1 50.0 109.50 ! CI CT OS 50.0 109.50 ! CI CT CT 40.0 109.50 ! OS CI H1 50.0 109.50 ! OS CI CT 50.0 109.50 ! P OS CI 100.0 120.50 ! OH CI H1 50.0 109.50 ! OH CI CT 50.0 109.50 ! HO OH CI 55.0 108.50 ! !Added by Wei c3 c3 h1 46.4 110.07 ! From GAFF c3 c3 oh 67.7 109.43 c3 c3 c3 63.2 110.63 c3 c3 s4 68.324 111.460! From ANTECHAMBER c3 os c3 62.1 113.41 h2 c3 os 50.8 108.58 c3 c3 os 67.8 108.42 na c3 os 71.2 109.19 h1 c3 os 50.8 108.82 ca na cc 68.5 113.15 c3 na cc 62.6 125.09 c3 na ca 63.1 124.36 ca ca na 70.2 118.34 na ca nb 70.2 128.56 na cc nd 74.8 112.02 h5 cc na 49.8 122.10 h2 c3 na 50.3 107.66 c3 c3 na 65.8 112.59 ca ca nb 69.2 122.63 ca nd cc 71.1 108.82 ca ca nd 70.1 119.72 h5 cc nd 50.1 125.38 nb ca nb 71.2 125.84 h5 ca nb 51.8 116.35 ca nb ca 68.6 115.86 ca nh hn 49.6 113.79 nb ca nh 72.6 118.96 ca ca nh 69.3 120.13 hn nh hn 40.1 114.43 c3 oh ho 47.1 108.16 c3 c3 h2 46.0 111.59 h1 c3 oh 51.0 109.88 hx c3 n4 49.0 107.91 c c3 n4 65.8 111.54 c3 c3 n4 66.0 108.93 hn n4 hn 40.5 108.11 c3 c o 68.0 123.11 c3 c3 hc 46.4 110.05 c3 n4 hn 46.2 110.11 c3 c3 hx 46.0 111.74 c c3 c3 63.8 110.53 hc c3 hc 39.4 108.35 c3 s4 c3 62.1 96.82 h1 c3 h1 39.2 109.55 h1 c3 s4 42.9 108.66 c c3 hx 47.4 108.64 PHI X C C X 3.62500000 2 180.0 ! Junmei et al, 1999 X C CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 X C CB X 3.00000000 2 180.0 ! intrpol.bsd.on C6H6 X C CM X 2.17500000 2 180.0 ! intrpol.bsd.on C6H6 X C CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 X C N X 2.50000000 2 180.0 ! AA,NMA X C NS X 1.45000000 2 180.0 ! JCC,7,(1986),230 X C NA X 1.35000000 2 180.0 ! JCC,7,(1986),230 X C NC X 4.00000000 2 180.0 ! JCC,7,(1986),230 X C O X 2.80000000 2 180.0 ! Junmei et al, 1999 X C OH X 2.30000000 2 180.0 ! Junmei et al, 1999 X C OS X 2.70000000 2 180.0 ! Junmei et al, 1999 X CA CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 X CA CB X 3.50000000 2 180.0 ! intrpol.bsd.on C6H6 X CA CM X 2.55000000 2 180.0 ! intrpol.bsd.on C6H6 X CA CN X 3.62500000 2 180.0 ! reinterpolated 93' X CA CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 X CA N2 X 2.40000000 2 180.0 ! reinterpolated 93' X CA NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 X CA NC X 4.80000000 2 180.0 ! JCC,7,(1986),230 X CA OH X 0.90000000 2 180.0 ! Junmei et al, 99 X CB CB X 5.45000000 2 180.0 ! intrpol.bsd.on C6H6 X CB CN X 3.00000000 2 180.0 ! reinterpolated 93' X CB NS X 1.65000000 2 180.0 ! JCC,7,(1986),230 X CB NB X 2.55000000 2 180.0 ! JCC,7,(1986),230 X CB NC X 4.15000000 2 180.0 ! JCC,7,(1986),230 X CC CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 X CC CV X 5.15000000 2 180.0 ! intrpol.bsd.on C6H6 X CC CW X 5.37500000 2 180.0 ! intrpol.bsd.on C6H6 X CC NA X 1.40000000 2 180.0 ! JCC,7,(1986),230 X CC NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 X CD CD X 1.00000000 2 180.0 ! Junmei et al, 1999 X CD CT X 0.00000000 2 0.000 ! Junmei et al, 1999 X CD CM X 6.65000000 2 180.0 ! Junmei et al, 1999 X CK NS X 1.70000000 2 180.0 ! JCC,7,(1986),230 X CK NB X 10.0000000 2 180.0 ! JCC,7,(1986),230 X CM CM X 6.65000000 2 180.0 ! intrpol.bsd.on C6H6 X CM CT X 0.00000000 3 0.000 ! JCC,7,(1986),230 X CM NS X 1.85000000 2 180.0 ! JCC,7,(1986),230 X CM OS X 1.05000000 2 180.0 ! Junmei et al, 1999 X CN NA X 1.52500000 2 180.0 ! reinterpolated 93' X CQ NC X 6.80000000 2 180.0 ! JCC,7,(1986),230 X CT CT X 0.15555556 3 0.000 ! JCC,7,(1986),230 X CT CY X 0.00000000 1 0.000 ! Junmei et al, 1999 X CT CZ X 0.00000000 1 0.000 ! Junmei et al, 1999 X CT N X 0.00000000 2 0.000 ! JCC,7,(1986),230 X CT NS X 0.00000000 2 0.000 ! JCC,7,(1986),230 X CT N2 X 0.00000000 3 0.000 ! JCC,7,(1986),230 X CT NT X 0.30000000 3 0.000 ! Junmei et al, 1999 X CT N3 X 0.15555556 3 0.000 ! JCC,7,(1986),230 X CT OH X 0.16666667 3 0.000 ! JCC,7,(1986),230 X CT OS X 0.38333333 3 0.000 ! JCC,7,(1986),230 X CT S X 0.33333333 3 0.000 ! JCC,7,(1986),230 X CT SH X 0.25000000 3 0.000 ! JCC,7,(1986),230 X CS CB X 1.67500000 2 180.0 ! intrpol.bsd.onC6H6aa X CS CT X 0.00000000 2 0.000 ! JCC,7,(1986),230 X CS CW X 6.52500000 2 180.0 ! intrpol.bsd.on C6H6 X CR NA X 2.32500000 2 180.0 ! JCC,7,(1986),230 X CR NB X 5.00000000 2 180.0 ! JCC,7,(1986),230 X CV NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 X CW NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 X OH P X 0.25000000 3 0.000 ! JCC,7,(1986),230 X OS P X 0.25000000 3 0.000 ! JCC,7,(1986),230 N CT C N 1.70000000 1 180.0 ! N CT C N 2.00000000 2 180.0 ! C N CT C 0.85000000 2 180.0 ! C N CT C 0.80000000 1 0.000 ! CT CT N C 0.50000000 4 180.0 ! phi,psi,parm94 CT CT N C 0.15000000 3 180.0 ! phi,psi,parm94 CT CT N C 0.53000000 1 0.000 ! phi,psi,parm94 CT CT C N 0.10000000 4 0.000 ! phi,psi,parm94 CT CT C N 0.07000000 2 0.000 ! phi,psi,parm94 H N C O 2.50000000 2 180.0 ! JCC,7,(1986),230 H N C O 2.00000000 1 0.000 ! J.C.cistrans-NMA DE CT S S CT 3.50000000 2 0.000 ! JCC,7,(1986),230 CT S S CT 0.60000000 3 0.000 ! JCC,7,(1986),230 OH P OS CT 0.25000000 3 0.000 ! JCC,7,(1986),230 OH P OS CT 1.20000000 2 0.000 ! gg> ene.631g*/mp2 OS P OS CT 0.25000000 3 0.000 ! JCC,7,(1986),230 OS P OS CT 1.20000000 2 0.000 ! gg> ene.631g*/mp2 H1 CT C O 0.80000000 1 0.000 ! Junmei et al, 1999 H1 CT C O 0.08000000 3 180.0 ! Junmei et al, 1999 HC CT C O 0.80000000 1 0.000 ! Junmei et al, 1999 HC CT C O 0.08000000 3 180.0 ! Junmei et al, 1999 HC CT CT HC 0.15000000 3 0.000 ! Junmei et al, 1999 HC CT CT CT 0.16000000 3 0.000 ! Junmei et al, 1999 HC CT CM CM 0.38000000 3 180.0 ! Junmei et al, 1999 HC CT CM CM 1.15000000 1 0.000 ! Junmei et al, 1999 HO OH CT CT 0.16000000 3 0.000 ! Junmei et al, 1999 HO OH CT CT 0.25000000 1 0.000 ! Junmei et al, 1999 HO OH C O 2.30000000 2 180.0 ! Junmei et al, 1999 HO OH C O 1.90000000 1 0.000 ! Junmei et al, 1999 CM CM C O 2.17500000 2 180.0 ! Junmei et al, 1999 CM CM C O 0.30000000 3 0.000 ! Junmei et al, 1999 CT CM CM CT 6.65000000 2 180.0 ! Junmei et al, 1999 CT CM CM CT 1.90000000 1 180.0 ! Junmei et al, 1999 CT CT CT CT 0.18000000 3 0.000 ! Junmei et al, 1999 CT CT CT CT 0.25000000 2 180.0 ! Junmei et al, 1999 CT CT CT CT 0.20000000 1 180.0 ! Junmei et al, 1999 CT CT NT CT 0.30000000 3 0.000 ! Junmei et al, 1999 CT CT NT CT 0.48000000 2 180.0 ! Junmei et al, 1999 CT CT OS CT 0.38300000 3 0.000 ! CT CT OS CT 0.10000000 2 180.0 ! CT CT OS C 0.38300000 3 0.000 ! Junmei et al, 1999 CT CT OS C 0.80000000 1 180.0 ! Junmei et al, 1999 CT OS CT OS 0.10000000 3 0.000 ! Junmei et al, 1999 CT OS CT OS 0.85000000 2 180.0 ! Junmei et al, 1999 CT OS CT OS 1.35000000 1 180.0 ! Junmei et al, 1999 CT OS CT NS 0.38300000 3 0.000 ! parm98.dat, TC,PC,PAK CT OS CT NS 0.65000000 2 0.000 ! Piotr et al. CT CZ CZ HZ 0.00000000 1 0.000 ! Junmei et al, 1999 O C OS CT 2.70000000 2 180.0 ! Junmei et al, 1999 O C OS CT 1.40000000 1 180.0 ! Junmei et al, 1999 OS CT NS CK 0.00000000 2 0.000 ! parm98, TC,PC,PAK OS CT NS CK 2.50000000 1 0.000 ! parm98, TC,PC,PAK OS CT NS CM 0.00000000 2 0.000 ! parm98, TC,PC,PAK OS CT NS CM 2.50000000 1 0.000 ! parm98, TC,PC,PAK OS CT CT OS 0.14400000 3 0.000 ! parm98, TC,PC,PAK OS CT CT OS 1.17500000 2 0.000 ! Piotr et al. OS CT CT OH 0.14400000 3 0.000 ! parm98, TC,PC,PAK OS CT CT OH 1.17500000 2 0.000 ! parm98, TC,PC,PAK OH CT CT OH 0.14400000 3 0.000 ! parm98, TC,PC,PAK OH CT CT OH 1.17500000 2 0.000 ! parm98, TC,PC,PAK F CT CT F 1.20000000 1 180.0 ! Junmei et al, 1999 Cl CT CT Cl 0.45000000 1 180.0 ! Junmei et al, 1999 Br CT CT Br 0.00000000 1 180.0 ! Junmei et al, 1999 H1 CT CT OS 0.25000000 1 0.000 ! Junmei et al, 1999 H1 CT CT OH 0.25000000 1 0.000 ! Junmei et al, 1999 H1 CT CT F 0.19000000 1 0.000 ! Junmei et al, 1999 H1 CT CT Cl 0.25000000 1 0.000 ! Junmei et al, 1999 H1 CT CT Br 0.55000000 1 0.000 ! Junmei et al, 1999 HC CT CT OS 0.25000000 1 0.000 ! Junmei et al, 1999 HC CT CT OH 0.25000000 1 0.000 ! Junmei et al, 1999 HC CT CT F 0.19000000 1 0.000 ! Junmei et al, 1999 HC CT CT Cl 0.25000000 1 0.000 ! Junmei et al, 1999 HC CT CT Br 0.55000000 1 0.000 ! Junmei et al, 1999 H1 CT NT LP 0.00000000 3 0.000 ! CT CT NT LP 0.00000000 3 0.000 ! CT C N LP 0.00000000 2 180.0 ! O C N LP 0.00000000 2 180.0 ! H1 CT OH LP 0.00000000 3 0.0 ! CT CT OH LP 0.00000000 3 0.0 ! H1 CT OS LP 0.00000000 3 0.0 ! H2 CT OS LP 0.00000000 3 0.0 ! CT CT OS LP 0.00000000 3 0.0 ! CM CM OS LP 0.00000000 2 180.0 ! HA CM OS LP 0.00000000 2 180.0 ! H4 CM OS LP 0.00000000 2 180.0 ! ! BS0 Parameters with CI Perez et al. BJ 92: 3817 (2007) X CI OS X 0.3833 3 0.0 ! X CI OH X 0.1667 3 0.0 ! X CI CT X 0.1556 3 0.0 ! CT OS CT CI 0.383 3 0.0 ! CT OS CT CI 0.100 2 180.0 ! H1 CI CT OS 0.250 1 0.0 ! H1 CI CT OH 0.250 1 0.0 ! H1 CT CI OS 0.250 1 0.0 ! H1 CT CI OH 0.250 1 0.0 ! CI CT CT CT 0.180 3 0.0 ! CI CT CT CT 0.250 2 180.0 ! CI CT CT CT 0.200 1 180.0 ! OS P OS CI 0.185181 1 31.79508 ! alfa OS P OS CI 1.256531 2 351.95960 ! alfa OS P OS CI 0.354858 3 357.24748 ! alfa OH P OS CI 0.185181 1 31.79508 ! alfa OH P OS CI 1.256531 2 351.95960 ! alfa OH P OS CI 0.354858 3 357.24748 ! alfa CT CT CI OS 1.178040 1 190.97653 ! gamma CT CT CI OS 0.092102 2 295.63279 ! gamma CT CT CI OS 0.962830 3 348.09535 ! gamma CT CT CI OH 1.178040 1 190.97653 ! gamma CT CT CI OH 0.092102 2 295.63279 ! gamma CT CT CI OH 0.962830 3 348.09535 ! gamma ! Added by Wei c3 c3 c3 c3 0.18 3 0.0 c3 c3 c3 c3 0.25 2 180.0 c3 c3 c3 c3 0.20 1 180.0 X c3 c3 X 0.156 3 0.0 ho oh c3 c3 0.16 3 0.0 ! Junmei et al, 1999 ho oh c3 c3 0.25 1 0.0 ! Junmei et al, 1999 X c3 s4 X 0.20 3 0.0 c3 os c3 na 0.383 3 0.0 ! parm98.dat, TC,PC,PAK c3 os c3 na 0.65 2 0.0 ! Piotr et al. c3 c3 os c3 0.383 3 0.0 c3 c3 os c3 0.1 2 180.0 X c3 os X 0.383333 3 0.0 ! JCC,7,(1986),230 X c3 na X 0.000 2 0.0 ! JCC,7,(1986),230 X ca nb X 4.800 2 180.0 ! same as X-CA-NC-X X cc nd X 4.750 2 180.000 ! statistic value from parm94 X ca nh X 1.050 2 180.000 X ca nd X 4.800 2 180.0 ! same as X-CA-NC-X X c3 oh X 0.166667 3 0.000 ! JCC,7,(1986),230 X c c3 X 0.000 2 180.000 ! JCC, 7, (1986), 230 X c3 n4 X 0.155556 3 0.000 ! JCC,7,(1986),230 IMPHI X X C O 10.5 2 180.0 ! JCC,7,(1986),230 X O2 C O2 10.5 2 180.0 ! JCC,7,(1986),230 X X N H 1.0 2 180.0 ! JCC,7,(1986),230 X X N2 H 1.0 2 180.0 ! JCC,7,(1986),230 X X NA H 1.0 2 180.0 ! JCC,7,(1986),230 X N2 CA N2 10.5 2 180.0 ! JCC,7,(1986),230 X CT N CT 1.0 2 180.0 ! JCC,7,(1986),230 X X CA HA 1.1 2 180.0 ! bsd.on C6H6 nmodes X X CW H4 1.1 2 180.0 X X CR H5 1.1 2 180.0 X X CV H4 1.1 2 180.0 X X CQ H5 1.1 2 180.0 X X CK H5 1.1 2 180.0 X X CM H4 1.1 2 180.0 X X CM HA 1.1 2 180.0 X X CA H4 1.1 2 180.0 ! bsd.on C6H6 nmodes X X CA H5 1.1 2 180.0 ! bsd.on C6H6 nmodes CK CB NS CT 1 2 180.0 CM C NS CT 1 2 180.0 ! dac guess, 9/94 CM C CM CT 1.1 2 180.0 ! CT O C OH 10.5 2 180.0 NA CV CC CT 1.1 2 180.0 ! NB CW CC CT 1.1 2 180.0 ! NA CW CC CT 1.1 2 180.0 ! CW CB CS CT 1.1 2 180.0 ! CA CA CA CT 1.1 2 180.0 ! C CM CM CT 1.1 2 180.0 ! dac guess, 9/94 NC CM CA N2 1.1 2 180.0 ! dac guess, 9/94 CB NC CA N2 1.1 2 180.0 ! dac, 10/94 NA NC CA N2 1.1 2 180.0 ! dac, 10/94 CA CA C OH 1.1 2 180.0 ! (not used in tyr!) CA CA CA OH 1.1 2 180.0 ! in tyr H5 O C OH 1.1 2 180.0 ! Junmei et al.1999 H5 O C OS 1.1 2 180.0 ! CM CT CM HA 1.1 2 180.0 ! Junmei et al.1999 CA CA CA Br 1.1 2 180.0 ! Junmei et al.1999 CM H4 C O 1.1 2 180.0 ! Junmei et al.1999 C CT N H 1.1 2 180.0 ! Junmei et al.1999 C CT N O 1.1 2 180.0 ! Junmei et al.1999 !Added by Wei (From ANTECHAMBER) c3 o c o 1.1 2 180.0 ! General improper torsional angle (1 general atom type) c3 ca na cc 1.1 2 180.0 ! Using default value h5 na cc nd 1.1 2 180.0 ca ca ca nd 1.1 2 180.0 ca nb ca nh 1.1 2 180.0 ca hn nh hn 1.1 2 180.0 h5 nb ca nb 1.1 2 180.0 ca na ca nb 1.1 2 180.0 nh ca hn hn 1.1 2 180.0 c o c3 o 1.1 2 180.0 ! ! Note: the HO and HW parameters, although zero in Cornell et al. ! should not have a 0.0 vdw radius in CHARMM to avoid difficulties ! with the 0.0/0.0 in the FAST OFF van der Waal code... ! ! NOTE: the defaults chosen here are to match AMBER. It is not ! recommended that users actually run with GROUP based truncation ! and a switch. Better would be ATOM based FSHIFT VSHIFT NONBONDED NBXMOD 5 GROUP SWITCH CDIEL - CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 0.83333333 WMIN 1.4 ! Emin Rmin/2 Emin/2 Rmin (for 1-4's) ! (kcal/mol) (A) H 0.0 -0.015700 0.600000 0.0 -0.0078500 0.600000 ! Ferguson base pair geom. HO 0.0 -0.000000 0.000000 0.0 -0.0000000 0.000000 ! OPLS Jorgensen, JACS,110,(1988),1657 HS 0.0 -0.015700 0.600000 0.0 -0.0078500 0.600000 ! W. Cornell CH3SH --> CH3OH FEP HC 0.0 -0.015700 1.487000 0.0 -0.0078500 1.487000 ! OPLS H1 0.0 -0.015700 1.387000 0.0 -0.0078500 1.387000 ! Veenstra et al JCC,8,(1992),963 H2 0.0 -0.015700 1.287000 0.0 -0.0078500 1.287000 ! Veenstra et al JCC,8,(1992),963 H3 0.0 -0.015700 1.187000 0.0 -0.0078500 1.187000 ! Veenstra et al JCC,8,(1992),963 HP 0.0 -0.015700 1.100000 0.0 -0.0078500 1.100000 ! Veenstra et al JCC,8,(1992),963 HA 0.0 -0.015000 1.459000 0.0 -0.0075000 1.459000 ! Spellmeyer H4 0.0 -0.015000 1.409000 0.0 -0.0075000 1.409000 ! Spellmeyer, one electrowithdr. neighbor H5 0.0 -0.015000 1.359000 0.0 -0.0075000 1.359000 ! Spellmeyer, two electrowithdr. neighbor HW 0.0 -0.000000 0.000000 0.0 -0.0000000 0.000000 ! TIP3P water model HZ 0.0 -0.015000 1.459000 0.0 -0.0075000 1.459000 ! H bonded to sp C (Howard et al JCC 16) O 0.0 -0.210000 1.661200 0.0 -0.1050000 1.661200 ! OPLS O2 0.0 -0.210000 1.661200 0.0 -0.1050000 1.661200 ! OPLS OW 0.0 -0.152000 1.768300 0.0 -0.0760000 1.768300 ! TIP3P water model OH 0.0 -0.210400 1.721000 0.0 -0.1052000 1.721000 ! OPLS OS 0.0 -0.170000 1.683700 0.0 -0.0850000 1.683700 ! OPLS ether CS 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! Spellmeyer CT 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! Spellmeyer C 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CA 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CM 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CB 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CC 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CN 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CK 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CQ 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CW 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CV 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CR 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CY 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CD 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS CZ 0.0 -0.086000 1.908000 0.0 -0.0430000 1.908000 ! OPLS N* 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! OPLS ! NY 0.0 -0.170000 1.824000 0.0 -0.0850000 1.824000 ! N in nitrile S 0.0 -0.250000 2.000000 0.0 -0.1250000 2.000000 ! W. Cornell CH3SH and CH3SCH3 FEP's SH 0.0 -0.250000 2.000000 0.0 -0.1250000 2.000000 ! W. Cornell CH3SH and CH3SCH3 FEP's P 0.0 -0.200000 2.100000 0.0 -0.1000000 2.100000 ! JCC,7,(1986),230; IM 0.0 -0.100000 2.470000 0.0 -0.0500000 2.470000 ! Cl- Smith & Dang, JCP 1994,100:5,3757 Li 0.0 -0.018300 1.137000 0.0 -0.0091500 1.137000 ! Li+ Aqvist JPC 1990,94,8021. (adapted) IP 0.0 -0.002770 1.868000 0.0 -0.0013850 1.868000 ! Na+ Aqvist JPC 1990,94,8021. (adapted) K 0.0 -0.000328 2.658000 0.0 -0.0001640 2.658000 ! K+ Aqvist JPC 1990,94,8021. (adapted) Rb 0.0 -0.000170 2.956000 0.0 -0.0000850 2.956000 ! Rb+ Aqvist JPC 1990,94,8021. (adapted) Es 0.0 -0.000081 3.395000 0.0 -0.0000403 3.395000 ! Cs+ Aqvist JPC 1990,94,8021. (adapted) MG 0.0 -0.894700 0.792600 0.0 -0.4473500 0.792600 ! Mg2+ Aqvist JPC 1990,94,8021.(adapted) C0 0.0 -0.459789 1.713100 0.0 -0.2298945 1.713100 ! Ca2+ Aqvist JPC 1990,94,8021.(adapted) Zn 0.0 -0.012500 1.100000 0.0 -0.0062500 1.100000 ! Zn2+, Merz,PAK, JACS,113,8262,(1991) F 0.0 -0.061000 1.750000 0.0 -0.0305000 1.750000 ! Gough et al. JCC 13,(1992),963. Cl 0.0 -0.265000 1.948000 0.0 -0.1325000 1.948000 ! Fox, JPCB,102,8070,(98),flex.mdl CHCl3 Br 0.0 -0.320000 2.220000 0.0 -0.1600000 2.220000 ! Junmei(?) I 0.0 -0.400000 2.350000 0.0 -0.2000000 2.350000 ! JCC,7,(1986),230; IB 0.0 -0.100000 5.000000 0.0 -0.0500000 5.000000 ! solvated ion for vacuum approximation LP 0.0 -0.000000 0.000000 0.0 -0.0000000 0.000000 ! lone pair CI 0.0 -0.1094 1.9080 0.0 -0.0547000 1.908000 ! Spellmeyer !Added by Wei hn 0.0 -0.015700 0.600000 0.0 -0.0078500 0.600000 ! Ferguson base pair geom. c3 0.0 -0.109400 1.908000 0.0 -0.0547000 1.908000 ! OPLS hx 0.0 -0.015700 1.100000 0.0 -0.0078500 1.100000 ! Veenstra et al JCC,8,(1992),963 s4 0.0 -0.250000 2.000000 0.0 -0.1250000 2.000000 ! OPLS END