* AMBER parm99SB force field conversion * See: Protiens: Str. Func. and Bioinfo. 65, 712 (2006) * ! ! This is a hand-conversion of the parm99SB force field ! based on the parm99-all.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 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 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 0.00000000 4 0.0 ! Simerling (2006) N CT C N 0.55000000 3 180.0 ! Simerling (2006) N CT C N 1.58000000 2 180.0 ! Simerling (2006) N CT C N 0.45000000 1 180.0 ! Simerling (2006) C N CT C 0.00000000 4 0.0 ! Simerling (2006) C N CT C 0.42000000 3 0.0 ! Simerling (2006) C N CT C 0.27000000 2 0.0 ! Simerling (2006) C N CT C 0.00000000 1 0.000 ! Simerling (2006) CT CT N C 0.00000000 4 0.000 ! Simerling (2006) CT CT N C 0.40000000 3 0.000 ! Simerling (2006) CT CT N C 2.00000000 2 0.000 ! Simerling (2006) CT CT N C 2.00000000 1 0.000 ! Simerling (2006) CT CT C N 0.00000000 4 0.000 ! Simerling (2006) CT CT C N 0.40000000 3 0.000 ! Simerling (2006) CT CT C N 0.20000000 2 0.000 ! Simerling (2006) CT CT C N 0.20000000 1 0.000 ! Simerling (2006) 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 ! 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 ! ! 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 END