* AMBER Cornell et al. (parm94) force field conversion * See: JACS (1995) 117, 5179-5197. * nucleic acid part converted by tec3, march 1997 * protein part converted by tec3, feb 1999 * ! ! 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). ! BONDS OW HW 553.0 0.9572 ! TIP3P water HW HW 553.0 1.5136 ! TIP3P water C CA 469.0 1.409 ! JCC,7,(1986),230; 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 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; TYR 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 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 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 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 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 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 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 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 CS HC 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes, not needed AA C N 490.0 1.335 ! JCC,7,(1986),230; 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 CA CN 469.0 1.400 ! 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 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 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 H N 434.0 1.010 ! JCC,7,(1986),230; AA H N3 434.0 1.010 ! JCC,7,(1986),230; LYS HS SH 274.0 1.336 ! JCC,7,(1986),230; CYS S S 166.0 2.038 ! JCC,7,(1986),230; CYX (SCHERAGA) CT F 367.0 1.380 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 THETAS HW OW HW 100. 104.52 ! TIP3P water HW HW OW 0. 127.74 ! (found in crystallographic water with 3 bonds) 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 OH 70.0 117.00 ! 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 ! CT C N 70.0 116.60 ! AA general N C O 80.0 122.90 ! AA general O C O 80.0 126.00 ! AA COO terminal residues O2 C O2 80.0 126.00 ! AA GLU (SCH JPC 79,2379) O C OH 80.0 126.00 ! CA C CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA tyr CA C OH 70.0 120.00 ! AA tyr C CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes 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 35.0 120.00 ! CA CA H4 35.0 120.00 ! CB CA HA 35.0 120.00 ! CB CA H4 35.0 120.00 ! 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 ! N2 CA NA 70.0 116.00 ! N2 CA NC 70.0 119.30 ! NA CA NC 70.0 123.30 ! C CA HA 35.0 120.00 ! AA tyr N2 CA N2 70.0 120.00 ! AA arg CN CA HA 35.0 120.00 ! AA trp CA CA CN 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA trp 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 ! NS CB NC 70.0 126.20 ! 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 H5 CK NS 35.0 123.05 ! H5 CK NB 35.0 123.05 ! 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 35.0 119.70 ! C CM H4 35.0 119.70 ! CA CM CM 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt CA CM HA 35.0 123.30 ! CA CM H4 35.0 123.30 ! CM CM CT 70.0 119.70 ! CM CM HA 35.0 119.70 ! CM CM H4 35.0 119.70 ! CM CM NS 70.0 121.20 ! H4 CM NS 35.0 119.10 ! H5 CQ NC 35.0 115.45 ! NC CQ NC 70.0 129.10 ! CM CT HC 50.0 109.50 ! changed based on NMA nmodes 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 ! HC CT HC 35.0 109.50 ! H1 CT H1 35.0 109.50 ! HP CT HP 35.0 109.50 ! AA lys, ch3nh4+ H2 CT NS 50.0 109.50 ! changed based on NMA nmodes 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 H2 CT OS 50.0 109.50 ! changed based on NMA nmodes NS CT OS 50.0 109.50 ! H1 CT N 50.0 109.50 ! AA general changed based on NMA nmodes 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 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 CT CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428) CT CT SH 50.0 108.60 ! AA cys H2 CT H2 35.0 109.50 ! AA lys H1 CT N2 50.0 109.50 ! AA arg changed based on NMA nmodes HP CT N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes CA CT CT 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379) C CT HC 50.0 109.50 ! AA gln changed based on NMA nmodes C CT N 63.0 110.10 ! AA general 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) C CT CT 63.0 111.10 ! AA general CA CT HC 50.0 109.50 ! AA tyr changed based on NMA nmodes CT CT N3 80.0 111.20 ! AA lys (JCP 76, 1439) CC CT CT 63.0 113.10 ! AA his CC CT HC 50.0 109.50 ! AA his changed based on NMA nmodes C CT N3 80.0 111.20 ! AA amino terminal residues CS CT CT 63.0 115.60 ! AA trp CS CT HC 50.0 109.50 ! AA trp changed based on NMA nmodes 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 35.0 120.00 ! AA his H5 CR NB 35.0 120.00 ! AA his NA CR NA 70.0 120.00 ! AA his NA CR NB 70.0 120.00 ! AA his CC CV H4 35.0 120.00 ! AA his CC CV NB 70.0 120.00 ! AA his H4 CV NB 35.0 120.00 ! AA his CC CW H4 35.0 120.00 ! AA his CC CW NA 70.0 120.00 ! AA his H4 CW NA 35.0 120.00 ! AA his CS CW H4 35.0 120.00 ! AA trp CS CW NA 70.0 108.70 ! AA trp CT CS CW 70.0 125.00 ! AA trp 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 CA CN NA 70.0 132.80 ! AA trp CB CN NA 70.0 104.40 ! AA trp CA CN CB 63.0 122.70 ! changed from 85.0 bsd on C6H6 nmodes; AA trp C N CT 50.0 121.90 ! AA general C N H 30.0 120.00 ! AA general, gln, asn,changed based on NMA nmodes CT N H 30.0 118.04 ! 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 30.0 119.20 ! changed based on NMA nmodes CB NS CK 70.0 105.40 ! CB NS CT 70.0 125.80 ! CB NS H 30.0 125.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes CK NS CT 70.0 128.80 ! CK NS H 30.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes CM NS CT 70.0 121.20 ! CM NS H 30.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes CA N2 H 35.0 120.00 ! H N2 H 35.0 120.00 ! CT N2 H 35.0 118.40 ! AA arg CA N2 CT 50.0 123.20 ! AA arg 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) C NA C 70.0 126.40 ! C NA CA 70.0 125.20 ! C NA H 30.0 116.80 ! changed based on NMA nmodes CA NA H 30.0 118.00 ! changed based on NMA nmodes CC NA CR 70.0 120.00 ! AA his CC NA H 30.0 120.00 ! AA his, changed based on NMA nmodes CR NA CW 70.0 120.00 ! AA his CR NA H 30.0 120.00 ! AA his, changed based on NMA nmodes CW NA H 30.0 120.00 ! AA his, changed based on NMA nmodes CN NA CW 70.0 111.60 ! AA trp CN NA H 30.0 123.10 ! 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 35.0 113.00 ! CT OH HO 55.0 108.50 ! HO OH P 45.0 108.50 ! 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 F CT F 77.0 109.10 ! JCC,13,(1992),963; F CT H1 35.0 109.50 ! JCC,13,(1992),963; PHI 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 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 OH X 0.90000000 2 180.0 ! JCC,7,(1986),230 X C CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 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 CT X 0.00000000 2 0.0 ! 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 CB CB X 5.45000000 2 180.0 ! intrpol.bsd.on C6H6 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 CK NS X 1.70000000 2 180.0 ! JCC,7,(1986),230 X CK NB X 10.00000000 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 0.0 ! JCC,7,(1986),230 X CM NS X 1.85000000 2 180.0 ! JCC,7,(1986),230 X CQ NC X 6.80000000 2 180.0 ! JCC,7,(1986),230 X CT CT X 0.15555556 3 0.0 ! JCC,7,(1986),230 X CT N X 0.00000000 2 0.0 ! JCC,7,(1986),230 X CT NS X 0.00000000 2 0.0 ! JCC,7,(1986),230 X CT N2 X 0.00000000 3 0.0 ! JCC,7,(1986),230 X CT OH X 0.16666667 3 0.0 ! JCC,7,(1986),230 X CT OS X 0.38333333 3 0.0 ! JCC,7,(1986),230 X OH P X 0.25000000 3 0.0 ! JCC,7,(1986),230 X OS P X 0.25000000 3 0.0 ! JCC,7,(1986),230 X C N X 2.50000000 2 180.0 ! AA|check Wendy?&NMA X CT N3 X 0.15555556 3 0.0 ! JCC,7,(1986),230 X CT S X 0.33333333 3 0.0 ! JCC,7,(1986),230 X CT SH X 0.25000000 3 0.0 ! JCC,7,(1986),230 X CS CB X 1.67500000 2 180.0 ! intrpol.bsd.onC6H6aa X CS CT X 0.00000000 2 0.0 ! JCC,7,(1986),230 X CS CW X 6.52500000 2 180.0 ! intrpol.bsd.on C6H6 X CA CN X 3.62500000 2 180.0 ! reinterpolated 93' X CB CN X 3.00000000 2 180.0 ! reinterpolated 93' X CC CT X 0.00000000 2 0.0 ! 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 CN NA X 1.52500000 2 180.0 ! reinterpolated 93' 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 CT CT OS CT 0.38300000 3 0.0 ! CT CT OS CT 0.10000000 2 180.0 ! C N CT C 0.20000000 2 180.0 ! N CT C N 0.40000000 4 180.0 ! N CT C N 1.35000000 2 180.0 ! N CT C N 0.75000000 1 180.0 ! CT CT N C 0.50000000 4 180.0 ! CT CT N C 0.15000000 3 180.0 ! CT CT N C 0.53000000 1 0.0 ! CT CT C N 0.10000000 4 0.0 ! CT CT C N 0.07000000 2 0.0 ! H N C O 2.50000000 2 180.0 ! JCC,7,(1986),230 H N C O 2.00000000 1 0.0 ! J.C.cistrans-NMA DE CT S S CT 3.50000000 2 0.0 ! JCC,7,(1986),230 CT S S CT 0.60000000 3 0.0 ! JCC,7,(1986),230 OS CT CT OS 0.14400000 3 0.0 ! JCC,7,(1986),230 OS CT CT OS 1.00000000 2 0.0 ! pucker anal (93') OS CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230 OS CT CT OH 1.00000000 2 0.0 ! pucker anal (93') OH CT CT OH 0.14400000 3 0.0 ! JCC,7,(1986),230 OH CT CT OH 1.00000000 2 0.0 ! check glicolWC? puc OH P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230 OH P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2 OS P OS CT 0.25000000 3 0.0 ! JCC,7,(1986),230 OS P OS CT 1.20000000 2 0.0 ! gg> ene.631g*/mp2 OS CT NS CK 0.50000000 2 180.0 ! sugar frag calc (PC) OS CT NS CK 2.50000000 1 0.0 ! sugar frag calc (PC) OS CT NS CM 0.50000000 2 180.0 ! sugar frag calc (PC) OS CT NS CM 2.50000000 1 0.0 ! sugar frag calc (PC) IMPHI X X C O 10.50000000 2 180.0 ! JCC,7,(1986),230 X O2 C O2 10.50000000 2 180.0 ! JCC,7,(1986),230 X X N H 1.00000000 2 180.0 ! JCC,7,(1986),230 X X N2 H 1.00000000 2 180.0 ! JCC,7,(1986),230 X X NA H 1.00000000 2 180.0 ! JCC,7,(1986),230 X N2 CA N2 10.50000000 2 180.0 ! JCC,7,(1986),230 X CT N CT 1.00000000 2 180.0 ! JCC,7,(1986),230 X X CA HA 1.10000000 2 180.0 ! bsd.on C6H6 nmodes X X CW H4 1.10000000 2 180.0 ! X X CR H5 1.10000000 2 180.0 ! X X CV H4 1.10000000 2 180.0 ! X X CQ H5 1.10000000 2 180.0 ! X X CK H5 1.10000000 2 180.0 ! X X CM H4 1.10000000 2 180.0 ! X X CM HA 1.10000000 2 180.0 ! X X CA H4 1.10000000 2 180.0 ! bsd.on C6H6 nmodes X X CA H5 1.10000000 2 180.0 ! bsd.on C6H6 nmodes CK CB NS CT 1.00000000 2 180.0 ! CM C NS CT 1.00000000 2 180.0 ! dac guess, 9/94 CM C CM CT 1.10000000 2 180.0 ! CT O C OH 10.50000000 2 180.0 ! NA CV CC CT 1.10000000 2 180.0 ! NB CW CC CT 1.10000000 2 180.0 ! NA CW CC CT 1.10000000 2 180.0 ! CW CB CS CT 1.10000000 2 180.0 ! CA CA CA CT 1.10000000 2 180.0 ! C CM CM CT 1.10000000 2 180.0 ! dac guess, 9/94 NC CM CA N2 1.10000000 2 180.0 ! dac guess, 9/94 CB NC CA N2 1.10000000 2 180.0 ! dac, 10/94 NA NC CA N2 1.10000000 2 180.0 ! dac, 10/94 CA CA C OH 1.10000000 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 -0.0157 0.6000 0.0 -0.00785 0.6000 ! Ferguson base pair geom. HO 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! OPLS, JACS,110,(1988),1657 HS 0.0 -0.0157 0.6000 0.0 -0.00785 0.6000 ! W. Cornell CH3SH --> CH3OH FEP HC 0.0 -0.0157 1.4870 0.0 -0.00785 1.4870 ! OPLS H1 0.0 -0.0157 1.3870 0.0 -0.00785 1.3870 ! Veenstra JCC,8,(1992),963 H2 0.0 -0.0157 1.2870 0.0 -0.00785 1.2870 ! Veenstra JCC,8,(1992),963 H3 0.0 -0.0157 1.1870 0.0 -0.00785 1.1870 ! Veenstra JCC,8,(1992),963 HP 0.0 -0.0157 1.1000 0.0 -0.00785 1.1000 ! Veenstra JCC,8,(1992),963 HA 0.0 -0.0150 1.4590 0.0 -0.0075 1.4590 ! Spellmeyer H4 0.0 -0.0150 1.4090 0.0 -0.0075 1.4090 ! Spellmeyer, 1 e- withdr. nghbr H5 0.0 -0.0150 1.3590 0.0 -0.0075 1.3590 ! Spellmeyer, 2 e- withdr. nghbr HW 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! TIP3P water model O 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS O2 0.0 -0.2100 1.6612 0.0 -0.1050 1.6612 ! OPLS OW 0.0 -0.1520 1.7683 0.0 -0.0760 1.7683 ! TIP3P water model OH 0.0 -0.2104 1.7210 0.0 -0.1052 1.7210 ! OPLS OS 0.0 -0.1700 1.6837 0.0 -0.0850 1.6837 ! OPLS ether CT 0.0 -0.1094 1.9080 0.0 -0.0547 1.9080 ! Spellmeyer CA 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer C 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CM 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! Spellmeyer CS 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CB 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CC 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CN 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CK 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CQ 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CW 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CV 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CR 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CX 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CY 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS CD 0.0 -0.0860 1.9080 0.0 -0.0430 1.9080 ! OPLS N* 0.0 -0.1700 1.8240 0.0 -0.0850 1.8240 ! OPLS S 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's SH 0.0 -0.2500 2.0000 0.0 -0.1250 2.0000 ! Cornell CH3SH & CH3SCH3 FEP's P 0.0 -0.2000 2.1000 0.0 -0.1000 2.1000 ! JCC,7,(1986),230; IM 0.0 -0.1 2.47 0.0 -0.05 2.47 ! Cl- Smith, JCP 1994,100:5,3757 Li 0.0 -0.0183 1.1370 0.0 -0.00915 1.1370 ! Li+ Aqvist JPC 1990,94,8021. (adapted) IP 0.0 -0.00277 1.8680 0.0 -0.001385 1.8680 ! Na+ Aqvist JPC 1990,94,8021. (adapted) K 0.0 -0.000328 2.6580 0.0 -0.000164 2.6580 ! K+ Aqvist JPC 1990,94,8021. (adapted) Rb 0.0 -0.00017 2.9560 0.0 -0.000085 2.9560 ! Rb+ Aqvist JPC 1990,94,8021. (adapted) I 0.0 -0.40 2.35 0.0 -0.20 2.35 ! JCC,7,(1986),230; F 0.0 -0.061 1.75 0.0 -0.0305 1.75 ! Gough JCC 13,(1992),963. IB 0.0 -0.1 5.0 0.0 -0.05 5.0 ! solvated ion, vacuum apprx END