REMARKS * AMBER Cornell et al. (parm94) force field conversion REMARKS * See: JACS (1995) 117, 5179-5197. REMARKS * nucleic acid part converted by tec3, march 1997 REMARKS * protein part converted by tec3, feb 1999 REMARKS * set echo=false end ! ! This is a hand-conversion of the Cornell et. al. force field ! parm94.dat file (except for the torsion which were converted via ! a perl script). All the atom type names are the same except where ! otherwise noted. ! ! Any problems? Let me know... ! cheatham@helix.nih.gov, cheatham@cgl.ucsf.edu ! ! 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). ! BOND OW HW 553.0 0.9572 ! TIP3P water BOND HW HW 553.0 1.5136 ! TIP3P water BOND C CA 469.0 1.409 ! JCC,7,(1986),230; TYR BOND C CB 447.0 1.419 ! JCC,7,(1986),230; GUA BOND C CM 410.0 1.444 ! JCC,7,(1986),230; THY,URA BOND C CT 317.0 1.522 ! JCC,7,(1986),230; AA BOND C NS 424.0 1.383 ! JCC,7,(1986),230; CYT,URA BOND C NA 418.0 1.388 ! JCC,7,(1986),230; GUA.URA BOND C NC 457.0 1.358 ! JCC,7,(1986),230; CYT BOND C O 570.0 1.229 ! JCC,7,(1986),230; AA,CYT,GUA,THY,URA BOND C O2 656.0 1.250 ! JCC,7,(1986),230; GLU,ASP BOND C OH 450.0 1.364 ! JCC,7,(1986),230; TYR BOND CA CA 469.0 1.400 ! JCC,7,(1986),230; BENZENE,PHE,TRP,TYR BOND CA CB 469.0 1.404 ! JCC,7,(1986),230; ADE,TRP BOND CA CM 427.0 1.433 ! JCC,7,(1986),230; CYT BOND CA CT 317.0 1.510 ! JCC,7,(1986),230; PHE,TYR BOND CA HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR BOND CA H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; no assigned BOND CA N2 481.0 1.340 ! JCC,7,(1986),230; ARG,CYT,GUA BOND CA NA 427.0 1.381 ! JCC,7,(1986),230; GUA BOND CA NC 483.0 1.339 ! JCC,7,(1986),230; ADE,CYT,GUA BOND CB CB 520.0 1.370 ! JCC,7,(1986),230; ADE,GUA BOND CB NS 436.0 1.374 ! JCC,7,(1986),230; ADE,GUA BOND CB NB 414.0 1.391 ! JCC,7,(1986),230; ADE,GUA BOND CB NC 461.0 1.354 ! JCC,7,(1986),230; ADE,GUA BOND CK H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA BOND CK NS 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA BOND CK NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA BOND CM CM 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA BOND CM CT 317.0 1.510 ! JCC,7,(1986),230; THY BOND CM HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA BOND CM H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA BOND CM H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; not assigned BOND CM NS 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA BOND CQ H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE BOND CQ NC 502.0 1.324 ! JCC,7,(1986),230; ADE BOND CT CT 310.0 1.526 ! JCC,7,(1986),230; AA, SUGARS BOND CT HC 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, SUGARS BOND CT H1 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE BOND CT H2 340.0 1.090 ! changed from 331 bsd on NMA nmodes; SUGARS BOND CT H3 340.0 1.090 ! changed from 331 bsd on NMA nmodes; not assigned BOND CT HP 340.0 1.090 ! changed from 331; AA lysine, methyl ammonium cation BOND CT NS 337.0 1.475 ! JCC,7,(1986),230; ADE,CYT,GUA,THY,URA BOND CT N2 337.0 1.463 ! JCC,7,(1986),230; ARG BOND CT OH 320.0 1.410 ! JCC,7,(1986),230; SUGARS BOND CT OS 320.0 1.410 ! JCC,7,(1986),230; NUCLEIC ACIDS BOND H N2 434.0 1.010 ! JCC,7,(1986),230; ADE,CYT,GUA,ARG BOND H NS 434.0 1.010 ! for plain unmethylated bases ADE,CYT,GUA,ARG BOND H NA 434.0 1.010 ! JCC,7,(1986),230; GUA,URA,HIS BOND HO OH 553.0 0.960 ! JCC,7,(1986),230; SUGARS,SER,TYR BOND HO OS 553.0 0.960 ! JCC,7,(1986),230; NUCLEOTIDE ENDS BOND O2 P 525.0 1.480 ! JCC,7,(1986),230; NA PHOSPHATES BOND OH P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES BOND OS P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES BOND CS HC 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes, not needed AA BOND C N 490.0 1.335 ! JCC,7,(1986),230; AA BOND CS CB 388.0 1.459 ! JCC,7,(1986),230; TRP BOND CS CT 317.0 1.495 ! JCC,7,(1986),230; TRP BOND CS CW 546.0 1.352 ! JCC,7,(1986),230; TRP BOND CA CN 469.0 1.400 ! JCC,7,(1986),230; TRP BOND CB CN 447.0 1.419 ! JCC,7,(1986),230; TRP BOND CC CT 317.0 1.504 ! JCC,7,(1986),230; HIS BOND CC CV 512.0 1.375 ! JCC,7,(1986),230; HIS(delta) BOND CC CW 518.0 1.371 ! JCC,7,(1986),230; HIS(epsilon) BOND CC NA 422.0 1.385 ! JCC,7,(1986),230; HIS BOND CC NB 410.0 1.394 ! JCC,7,(1986),230; HIS BOND CN NA 428.0 1.380 ! JCC,7,(1986),230; TRP BOND CR H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS BOND CR NA 477.0 1.343 ! JCC,7,(1986),230; HIS BOND CR NB 488.0 1.335 ! JCC,7,(1986),230; HIS BOND CT N 337.0 1.449 ! JCC,7,(1986),230; AA BOND CT N3 367.0 1.471 ! JCC,7,(1986),230; LYS BOND CT S 227.0 1.810 ! changed from 222.0 based on dimethylS nmodes BOND CT SH 237.0 1.810 ! changed from 222.0 based on methanethiol nmodes BOND CV H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; HIS BOND CV NB 410.0 1.394 ! JCC,7,(1986),230; HIS BOND CW H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) BOND CW NA 427.0 1.381 ! JCC,7,(1986),230; HIS,TRP BOND H N 434.0 1.010 ! JCC,7,(1986),230; AA BOND H N3 434.0 1.010 ! JCC,7,(1986),230; LYS BOND HS SH 274.0 1.336 ! JCC,7,(1986),230; CYS BOND S S 166.0 2.038 ! JCC,7,(1986),230; CYX (SCHERAGA) BOND CT F 367.0 1.380 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 ANGLE HW OW HW 100. 104.52 ! TIP3P water ANGLE HW HW OW 0. 127.74 ! (found in crystallographic water with 3 bonds) ANGLE CB C NA 70.0 111.30 ! NA ANGLE CB C O 80.0 128.80 ! ANGLE CM C NA 70.0 114.10 ! ANGLE CM C O 80.0 125.30 ! ANGLE CT C O 80.0 120.40 ! ANGLE CT C O2 70.0 117.00 ! ANGLE CT C OH 70.0 117.00 ! ANGLE NS C NA 70.0 115.40 ! ANGLE NS C NC 70.0 118.60 ! ANGLE NS C O 80.0 120.90 ! ANGLE NA C O 80.0 120.60 ! ANGLE NC C O 80.0 122.50 ! ANGLE CT C N 70.0 116.60 ! AA general ANGLE N C O 80.0 122.90 ! AA general ANGLE O C O 80.0 126.00 ! AA COO terminal residues ANGLE O2 C O2 80.0 126.00 ! AA GLU (SCH JPC 79,2379) ANGLE O C OH 80.0 126.00 ! ANGLE CA C CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA tyr ANGLE CA C OH 70.0 120.00 ! AA tyr ANGLE C CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes ANGLE CA CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes ANGLE CA CA CB 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes ANGLE CA CA CT 70.0 120.00 ! ANGLE CA CA HA 35.0 120.00 ! ANGLE CA CA H4 35.0 120.00 ! ANGLE CB CA HA 35.0 120.00 ! ANGLE CB CA H4 35.0 120.00 ! ANGLE CB CA N2 70.0 123.50 ! ANGLE CB CA NC 70.0 117.30 ! ANGLE CM CA N2 70.0 120.10 ! ANGLE CM CA NC 70.0 121.50 ! ANGLE N2 CA NA 70.0 116.00 ! ANGLE N2 CA NC 70.0 119.30 ! ANGLE NA CA NC 70.0 123.30 ! ANGLE C CA HA 35.0 120.00 ! AA tyr ANGLE N2 CA N2 70.0 120.00 ! AA arg ANGLE CN CA HA 35.0 120.00 ! AA trp ANGLE CA CA CN 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA trp ANGLE C CB CB 63.0 119.20 ! changed from 85.0 bsd on C6H6 nmodes; NA gua ANGLE C CB NB 70.0 130.00 ! ANGLE CA CB CB 63.0 117.30 ! changed from 85.0 bsd on C6H6 nmodes; NA ade ANGLE CA CB NB 70.0 132.40 ! ANGLE CB CB NS 70.0 106.20 ! ANGLE CB CB NB 70.0 110.40 ! ANGLE CB CB NC 70.0 127.70 ! ANGLE NS CB NC 70.0 126.20 ! ANGLE CS CB CA 63.0 134.90 ! changed from 85.0 bsd on C6H6 nmodes; AA trp ANGLE CS CB CN 63.0 108.80 ! changed from 85.0 bsd on C6H6 nmodes; AA trp ANGLE CA CB CN 63.0 116.20 ! changed from 85.0 bsd on C6H6 nmodes; AA trp ANGLE H5 CK NS 35.0 123.05 ! ANGLE H5 CK NB 35.0 123.05 ! ANGLE NS CK NB 70.0 113.90 ! ANGLE C CM CM 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy ANGLE C CM CT 70.0 119.70 ! ANGLE C CM HA 35.0 119.70 ! ANGLE C CM H4 35.0 119.70 ! ANGLE CA CM CM 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt ANGLE CA CM HA 35.0 123.30 ! ANGLE CA CM H4 35.0 123.30 ! ANGLE CM CM CT 70.0 119.70 ! ANGLE CM CM HA 35.0 119.70 ! ANGLE CM CM H4 35.0 119.70 ! ANGLE CM CM NS 70.0 121.20 ! ANGLE H4 CM NS 35.0 119.10 ! ANGLE H5 CQ NC 35.0 115.45 ! ANGLE NC CQ NC 70.0 129.10 ! ANGLE CM CT HC 50.0 109.50 ! changed based on NMA nmodes ANGLE CT CT CT 40.0 109.50 ! ANGLE CT CT HC 50.0 109.50 ! changed based on NMA nmodes ANGLE CT CT H1 50.0 109.50 ! changed based on NMA nmodes ANGLE CT CT H2 50.0 109.50 ! changed based on NMA nmodes ANGLE CT CT HP 50.0 109.50 ! changed based on NMA nmodes ANGLE CT CT NS 50.0 109.50 ! ANGLE CT CT OH 50.0 109.50 ! ANGLE CT CT OS 50.0 109.50 ! ANGLE HC CT HC 35.0 109.50 ! ANGLE H1 CT H1 35.0 109.50 ! ANGLE HP CT HP 35.0 109.50 ! AA lys, ch3nh4+ ANGLE H2 CT NS 50.0 109.50 ! changed based on NMA nmodes ANGLE H1 CT NS 50.0 109.50 ! changed based on NMA nmodes ANGLE H1 CT OH 50.0 109.50 ! changed based on NMA nmodes ANGLE H1 CT OS 50.0 109.50 ! changed based on NMA nmodes ANGLE H2 CT OS 50.0 109.50 ! changed based on NMA nmodes ANGLE NS CT OS 50.0 109.50 ! ANGLE H1 CT N 50.0 109.50 ! AA general changed based on NMA nmodes ANGLE C CT H1 50.0 109.50 ! AA general changed based on NMA nmodes ANGLE C CT HP 50.0 109.50 ! AA zwitterion changed based on NMA nmodes ANGLE H1 CT S 50.0 109.50 ! AA cys changed based on NMA nmodes ANGLE H1 CT SH 50.0 109.50 ! AA cyx changed based on NMA nmodes ANGLE CT CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428) ANGLE CT CT SH 50.0 108.60 ! AA cys ANGLE H2 CT H2 35.0 109.50 ! AA lys ANGLE H1 CT N2 50.0 109.50 ! AA arg changed based on NMA nmodes ANGLE HP CT N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes ANGLE CA CT CT 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379) ANGLE C CT HC 50.0 109.50 ! AA gln changed based on NMA nmodes ANGLE C CT N 63.0 110.10 ! AA general ANGLE CT CT N2 80.0 111.20 ! AA arg (JCP 76, 1439) ANGLE CT CT N 80.0 109.70 ! AA ala, general (JACS 94, 2657) ANGLE C CT CT 63.0 111.10 ! AA general ANGLE CA CT HC 50.0 109.50 ! AA tyr changed based on NMA nmodes ANGLE CT CT N3 80.0 111.20 ! AA lys (JCP 76, 1439) ANGLE CC CT CT 63.0 113.10 ! AA his ANGLE CC CT HC 50.0 109.50 ! AA his changed based on NMA nmodes ANGLE C CT N3 80.0 111.20 ! AA amino terminal residues ANGLE CS CT CT 63.0 115.60 ! AA trp ANGLE CS CT HC 50.0 109.50 ! AA trp changed based on NMA nmodes ANGLE CT CC NA 70.0 120.00 ! AA his ANGLE CT CC CV 70.0 120.00 ! AA his ANGLE CT CC NB 70.0 120.00 ! AA his ANGLE CV CC NA 70.0 120.00 ! AA his ANGLE CW CC NA 70.0 120.00 ! AA his ANGLE CW CC NB 70.0 120.00 ! AA his ANGLE CT CC CW 70.0 120.00 ! AA his ANGLE H5 CR NA 35.0 120.00 ! AA his ANGLE H5 CR NB 35.0 120.00 ! AA his ANGLE NA CR NA 70.0 120.00 ! AA his ANGLE NA CR NB 70.0 120.00 ! AA his ANGLE CC CV H4 35.0 120.00 ! AA his ANGLE CC CV NB 70.0 120.00 ! AA his ANGLE H4 CV NB 35.0 120.00 ! AA his ANGLE CC CW H4 35.0 120.00 ! AA his ANGLE CC CW NA 70.0 120.00 ! AA his ANGLE H4 CW NA 35.0 120.00 ! AA his ANGLE CS CW H4 35.0 120.00 ! AA trp ANGLE CS CW NA 70.0 108.70 ! AA trp ANGLE CT CS CW 70.0 125.00 ! AA trp ANGLE CB CS CT 70.0 128.60 ! AA trp ANGLE CB CS CW 63.0 106.40 ! changed from 85.0 bsd on C6H6 nmodes; AA trp ANGLE CA CN NA 70.0 132.80 ! AA trp ANGLE CB CN NA 70.0 104.40 ! AA trp ANGLE CA CN CB 63.0 122.70 ! changed from 85.0 bsd on C6H6 nmodes; AA trp ANGLE C N CT 50.0 121.90 ! AA general ANGLE C N H 30.0 120.00 ! AA general, gln, asn,changed based on NMA nmodes ANGLE CT N H 30.0 118.04 ! AA general, changed based on NMA nmodes ANGLE CT N CT 50.0 118.00 ! AA pro (DETAR JACS 99,1232) ANGLE H N H 35.0 120.00 ! ade,cyt,gua,gln,asn ** ANGLE C NS CM 70.0 121.60 ! ANGLE C NS CT 70.0 117.60 ! ANGLE C NS H 30.0 119.20 ! changed based on NMA nmodes ANGLE CB NS CK 70.0 105.40 ! ANGLE CB NS CT 70.0 125.80 ! ANGLE CB NS H 30.0 125.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes ANGLE CK NS CT 70.0 128.80 ! ANGLE CK NS H 30.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes ANGLE CM NS CT 70.0 121.20 ! ANGLE CM NS H 30.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes ANGLE CA N2 H 35.0 120.00 ! ANGLE H N2 H 35.0 120.00 ! ANGLE CT N2 H 35.0 118.40 ! AA arg ANGLE CA N2 CT 50.0 123.20 ! AA arg ANGLE CT N3 H 50.0 109.50 ! AA lys, changed based on NMA nmodes ANGLE CT N3 CT 50.0 109.50 ! AA pro/nt ANGLE H N3 H 35.0 109.50 ! AA lys, AA(end) ANGLE C NA C 70.0 126.40 ! ANGLE C NA CA 70.0 125.20 ! ANGLE C NA H 30.0 116.80 ! changed based on NMA nmodes ANGLE CA NA H 30.0 118.00 ! changed based on NMA nmodes ANGLE CC NA CR 70.0 120.00 ! AA his ANGLE CC NA H 30.0 120.00 ! AA his, changed based on NMA nmodes ANGLE CR NA CW 70.0 120.00 ! AA his ANGLE CR NA H 30.0 120.00 ! AA his, changed based on NMA nmodes ANGLE CW NA H 30.0 120.00 ! AA his, changed based on NMA nmodes ANGLE CN NA CW 70.0 111.60 ! AA trp ANGLE CN NA H 30.0 123.10 ! AA trp, changed based on NMA nmodes ANGLE CB NB CK 70.0 103.80 ! ANGLE CC NB CR 70.0 117.00 ! AA his ANGLE CR NB CV 70.0 117.00 ! AA his ANGLE C NC CA 70.0 120.50 ! ANGLE CA NC CB 70.0 112.20 ! ANGLE CA NC CQ 70.0 118.60 ! ANGLE CB NC CQ 70.0 111.00 ! ANGLE C OH HO 35.0 113.00 ! ANGLE CT OH HO 55.0 108.50 ! ANGLE HO OH P 45.0 108.50 ! ANGLE CT OS CT 60.0 109.50 ! ANGLE CT OS P 100.0 120.50 ! ANGLE P OS P 100.0 120.50 ! ANGLE O2 P OH 45.0 108.23 ! ANGLE O2 P O2 140.0 119.90 ! ANGLE O2 P OS 100.0 108.23 ! ANGLE OH P OS 45.0 102.60 ! ANGLE OS P OS 45.0 102.60 ! ANGLE CT S CT 62.0 98.90 ! AA met ANGLE CT S S 68.0 103.70 ! AA cyx (SCHERAGA JPC 79,1428) ANGLE CT SH HS 43.0 96.00 ! changed from 44.0 based on methanethiol nmodes ANGLE HS SH HS 35.0 92.07 ! AA cys ANGLE F CT F 77.0 109.10 ! JCC,13,(1992),963; ANGLE F CT H1 35.0 109.50 ! JCC,13,(1992),963; DIHEDRAL X C CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X C N X 2.50000000 2 180.0 ! AA|check Wendy?&NMA DIHEDRAL X CT N X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL C N CT C 0.20000000 2 180.0 ! DIHEDRAL N CT C N MULTIPLE= 3 0.40000000 4 180.0 ! 1.35000000 2 180.0 ! 0.75000000 1 180.0 ! DIHEDRAL CT CT N C MULTIPLE= 3 0.50000000 4 180.0 ! 0.15000000 3 180.0 ! 0.53000000 1 0.0 ! DIHEDRAL CT CT C N MULTIPLE= 2 0.10000000 4 0.0 ! 0.07000000 2 0.0 ! DIHEDRAL H N C O MULTIPLE= 2 2.50000000 2 180.0 ! JCC,7,(1986),230 2.00000000 1 0.0 ! J.C.cistrans-NMA DE DIHEDRAL CT S S CT MULTIPLE= 2 3.50000000 2 0.0 ! JCC,7,(1986),230 0.60000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL CT CT OS CT 0.38300000 3 0.0 ! DIHEDRAL CT CT OS CT 0.10000000 2 180.0 ! DIHEDRAL OS CT CT OS 0.14400000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL OS CT CT OS 1.00000000 2 0.0 ! pucker anal (93') DIHEDRAL OS CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL OS CT CT OH 1.00000000 2 0.0 ! pucker anal (93') DIHEDRAL OH CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL OH CT CT OH 1.00000000 2 0.0 ! check glicolWC? puc DIHEDRAL OH P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL OH P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2 DIHEDRAL OS P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL OS P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2 DIHEDRAL OS CT NS CK 0.50000000 2 180.0 ! sugar frag calc (PC) DIHEDRAL OS CT NS CK 2.50000000 1 0.0 ! sugar frag calc (PC) DIHEDRAL OS CT NS CM 0.50000000 2 180.0 ! sugar frag calc (PC) DIHEDRAL OS CT NS CM 2.50000000 1 0.0 ! sugar frag calc (PC) DIHEDRAL X C CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X C CB X 3.00000000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X C CM X 2.17500000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X C NS X 1.45000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X C NA X 1.35000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X C NC X 4.00000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X C OH X 0.90000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X C CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X CA CA X 3.62500000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CA CB X 3.50000000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CA CM X 2.55000000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CA CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X CA N2 X 2.40000000 2 180.0 ! reinterpolated 93' DIHEDRAL X CA NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CA NC X 4.80000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CB CB X 5.45000000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CB NS X 1.65000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CB NB X 2.55000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CB NC X 4.15000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CK NS X 1.70000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CK NB X 10.00000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CM CM X 6.65000000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CM CT X 0.00000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X CM NS X 1.85000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CQ NC X 6.80000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CT CT X 0.15555556 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X CT N X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X CT NS X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X CT N2 X 0.00000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X CT OH X 0.16666667 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X CT OS X 0.38333333 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X OH P X 0.25000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X OS P X 0.25000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X C N X 2.50000000 2 180.0 ! AA|check Wendy?&NMA DIHEDRAL X CT N3 X 0.15555556 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X CT S X 0.33333333 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X CT SH X 0.25000000 3 0.0 ! JCC,7,(1986),230 DIHEDRAL X CS CB X 1.67500000 2 180.0 ! intrpol.bsd.onC6H6aa DIHEDRAL X CS CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X CS CW X 6.52500000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CA CN X 3.62500000 2 180.0 ! reinterpolated 93' DIHEDRAL X CB CN X 3.00000000 2 180.0 ! reinterpolated 93' DIHEDRAL X CC CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X CC CV X 5.15000000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CC CW X 5.37500000 2 180.0 ! intrpol.bsd.on C6H6 DIHEDRAL X CC NA X 1.40000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CC NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CN NA X 1.52500000 2 180.0 ! reinterpolated 93' DIHEDRAL X CR NA X 2.32500000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CR NB X 5.00000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CV NB X 2.40000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X CW NA X 1.50000000 2 180.0 ! JCC,7,(1986),230 DIHEDRAL X C CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 DIHEDRAL X C N X 2.50000000 2 180.0 ! AA|check Wendy?&NMA DIHEDRAL X CT N X 0.00000000 2 0.0 ! JCC,7,(1986),230 IMPROPER CK CB NS CT 1.00000000 2 180.0 ! IMPROPER CM C NS CT 1.00000000 2 180.0 ! dac guess, 9/94 IMPROPER CM C CM CT 1.10000000 2 180.0 ! IMPROPER CT O C OH 10.50000000 2 180.0 ! IMPROPER NA CV CC CT 1.10000000 2 180.0 ! IMPROPER NB CW CC CT 1.10000000 2 180.0 ! IMPROPER NA CW CC CT 1.10000000 2 180.0 ! IMPROPER CW CB CS CT 1.10000000 2 180.0 ! IMPROPER CA CA CA CT 1.10000000 2 180.0 ! IMPROPER C CM CM CT 1.10000000 2 180.0 ! dac guess, 9/94 IMPROPER NC CM CA N2 1.10000000 2 180.0 ! dac guess, 9/94 IMPROPER CB NC CA N2 1.10000000 2 180.0 ! dac, 10/94 IMPROPER NA NC CA N2 1.10000000 2 180.0 ! dac, 10/94 IMPROPER CA CA C OH 1.10000000 2 180.0 ! IMPROPER X X C O 10.50000000 2 180.0 ! JCC,7,(1986),230 IMPROPER X O2 C O2 10.50000000 2 180.0 ! JCC,7,(1986),230 IMPROPER X X N H 1.00000000 2 180.0 ! JCC,7,(1986),230 IMPROPER X X N2 H 1.00000000 2 180.0 ! JCC,7,(1986),230 IMPROPER X X NA H 1.00000000 2 180.0 ! JCC,7,(1986),230 IMPROPER X N2 CA N2 10.50000000 2 180.0 ! JCC,7,(1986),230 IMPROPER X CT N CT 1.00000000 2 180.0 ! JCC,7,(1986),230 IMPROPER X X CA HA 1.10000000 2 180.0 ! bsd.on C6H6 nmodes IMPROPER X X CW H4 1.10000000 2 180.0 ! IMPROPER X X CR H5 1.10000000 2 180.0 ! IMPROPER X X CV H4 1.10000000 2 180.0 ! IMPROPER X X CQ H5 1.10000000 2 180.0 ! IMPROPER X X CK H5 1.10000000 2 180.0 ! IMPROPER X X CM H4 1.10000000 2 180.0 ! IMPROPER X X CM HA 1.10000000 2 180.0 ! IMPROPER X X CA H4 1.10000000 2 180.0 ! bsd.on C6H6 nmodes IMPROPER X X CA H5 1.10000000 2 180.0 ! bsd.on C6H6 nmodes ! ! 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 {* nonbonding parameter section *} {* ============================ *} nbonds atom cdie shift eps=1.0 e14fac=0.4 tolerance=0.5 cutnb=9.0 ctonnb=7.5 ctofnb=8.0 nbxmod=5 vswitch wmin 1.0 end ! Emin sigma Emin/2 sigma ! (kcal/mol) (A) (for 1-4's) NONBonded H 0.015700 1.069078 0.007850 1.069078 7.2382 0.9435 NONBonded HO 0.000000 1.069078 0.000000 1.069078 2.1447 0.6035 NONBonded HS 0.015700 1.069078 0.007850 1.069078 2.1447 0.6035 NONBonded HC 0.015700 2.649532 0.007850 2.649532 9.2028 1.0285 NONBonded H1 0.015700 2.471352 0.007850 2.471352 9.2028 1.0285 NONBonded H2 0.015700 2.293173 0.007850 2.293173 9.2028 1.0285 NONBonded H3 0.015700 2.114993 0.007850 2.114993 9.2028 1.0285 NONBonded HP 0.015700 1.959977 0.007850 1.959977 9.2028 1.0285 NONBonded HA 0.015000 2.599642 0.007500 2.599642 9.2028 1.0285 NONBonded H4 0.015000 2.510552 0.007500 2.510552 9.2028 1.0285 NONBonded H5 0.015000 2.421462 0.007500 2.421462 9.2028 1.0285 NONBonded HW 0.000000 1.069078 0.000000 1.069078 2.1447 0.6035 NONBonded O 0.210000 2.959921 0.105000 2.959921 14.1372 1.1985 NONBonded O2 0.210000 2.959921 0.105000 2.959921 14.1372 1.1985 NONBonded OW 0.152000 3.150752 0.076000 3.150752 14.1372 1.1985 NONBonded OH 0.210400 3.066473 0.105200 3.066473 14.1372 1.1985 NONBonded OS 0.170000 3.000012 0.085000 3.000012 14.1372 1.1985 NONBonded CT 0.109400 3.399669 0.054700 3.399669 20.5796 1.1592 NONBonded CA 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded C 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CM 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CS 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CB 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CC 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CN 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CK 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CQ 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CW 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CV 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CR 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CX 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CY 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded CD 0.086000 3.399669 0.043000 3.399669 20.5796 1.1592 NONBonded N* 0.170000 3.249998 0.085000 3.249998 15.5986 1.1534 NONBonded N 0.170000 3.249998 0.085000 3.249998 15.5986 1.1534 NONBonded N2 0.170000 3.249998 0.085000 3.249998 15.5986 1.1534 NONBonded N3 0.170000 3.249998 0.085000 3.249998 15.5986 1.1534 NONBonded NA 0.170000 3.249998 0.085000 3.249998 15.5986 1.1534 NONBonded NB 0.170000 3.249998 0.085000 3.249998 15.5986 1.1534 NONBonded S 0.250000 3.563594 0.125000 3.563594 24.4291 1.6416 NONBonded SH 0.250000 3.563594 0.125000 3.563594 24.4291 1.6416 NONBonded P 0.200000 3.741774 0.100000 3.741774 1.85 1.5136 NONBonded IM 0.100000 4.401039 0.050000 4.401039 1. 1. ! Cl- Smith, JCP 1994,100:5,3757 NONBonded Li 0.018300 2.025903 0.009150 2.025903 1. 1. ! Li+ Aqvist JPC 1990,94,8021. (adapted) NONBonded IP 0.002770 3.328397 0.001385 3.328397 1. 1. ! Na+ Aqvist JPC 1990,94,8021. (adapted) NONBonded K 0.000328 4.736016 0.000164 4.736016 1. 1. ! K+ Aqvist JPC 1990,94,8021. (adapted) NONBonded Rb 0.000170 5.266992 0.000085 5.266992 1. 1. ! Rb+ Aqvist JPC 1990,94,8021. (adapted) NONBonded I 0.400000 4.187223 0.200000 4.187223 1. 1. ! JCC,7,(1986),230; NONBonded F 0.061000 3.118145 0.030500 3.118145 1.47 1.2144 ! Gough JCC 13,(1992),963. NONBonded IB 0.100000 8.908985 0.050000 8.908985 1. 1. ! solvated ion, vacuum apprx set echo=true end