* - parameter file PARAM19 - * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 * !* - PEPTIDE GEOMETRY TO GIVE RAMACHANDRAN ET AL BBA 359:298 (1974) !* - PEPTIDE TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) !* - NONBONDED TERMS JORGENSEN JACS 103:3976 W/ RC1-4 = 1.80 EC1-4 = 0.1 !* The default h-bond exponents are now 6-repul 4-attr !* ++++++++ ATOMTYPE OS (IN METHYL ESTER) ADDED FOR CHARMM COURSE /LN ++++ !* SOLVENT PARAMETERS: SUPPORTING ST2 AND MODIFIED TIP3P MODEL !* Switched from Slater-Kirkwood to simple mixing rules - AB !* Hbond parameters based on comparisons of dimer results with !* ab initio calculations. - WER 12/19/84 !* Grouping of atom types for VDW parameters - BRB 1/3/85 !* !references !Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D. !Thesis, Department of Chemistry, Harvard University, Cambridge, MA, !USA, 1985 ! !and ! !Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free !Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105: !1902-21. BOND C C 450.0 1.38! FROM B. R. GELIN THESIS AMIDE AND DIPEPTIDES C CH1E 405.0 1.52! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT C CH2E 405.0 1.52! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED C CH3E 405.0 1.52 C CR1E 450.0 1.38 C CT 405.0 1.53 C N 471.0 1.33 C NC2 400.0 1.33! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE C NH1 471.0 1.33 C NH2 471.0 1.33 C NP 471.0 1.33 C NR 471.0 1.33 C O 580.0 1.23 C OC 580.0 1.23! FORCE DECREASE AND LENGTH INCREASE FROM C O C OH1 450.0 1.38! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) C OS 292.0 1.43! FROM DEP NORMAL MODE FIT CH1E CH1E 225.0 1.53 CH1E CH2E 225.0 1.52 CH1E CH3E 225.0 1.52 CH1E N 422.0 1.45 CH1E NH1 422.0 1.45 CH1E NH2 422.0 1.45 CH1E NH3 422.0 1.45 CH1E OH1 400.0 1.42! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) CH2E CH2E 225.0 1.52 CH2E CH3E 225.0 1.54 CH2E CR1E 250.0 1.45! FROM WARSHEL AND KARPLUS 1972 JACS 96:5612 CH2E N 422.0 1.45 CH2E NH1 422.0 1.45 CH2E NH2 422.0 1.45 CH2E NH3 422.0 1.45 CH2E OH1 400.0 1.42 CH2E S 450.0 1.81! FROM PARMFIX9 CH2E SH1E 450.0 1.81 CH3E NH1 422.0 1.49 CH3E NR 422.0 1.49 ! FOR NETROPSIN CH3E S 450.0 1.77! FROM PARMFIX9 CH3E OS 292.0 1.38! FROM DEP NORMAL MODE FIT CM OM 1115.0 1.128! FROM CAUGHEY ET AL(1978),CARBON MONOXIDE CR1E CR1E 450.0 1.38 CR1E NH1 450.0 1.305 CR1E NR 450.0 1.305 CT CT 200.0 1.53 CT N 422.0 1.45 CT NC2 422.0 1.45 CT NH1 422.0 1.45 CT NH2 422.0 1.45 CT NH3 422.0 1.45 CT OH1 400.0 1.42 CT S 450.0 1.81 FE CM 258.0 1.79! FROM KROEKER ET AL(JCP:72:4846) FE NP 500.0 2.09 FE NR 65.0 1.98! FROM NAGAI ET AL(1980) FE OM 250.0 1.8! JUST A GUESS. H NH1 405.0 0.98! GELIN AND IR STRETCH 3200 CM 1 H NH2 405.0 0.98 H OH1 450.0 0.96! FROM IR STRETCH 3400 CM 1 H OH2 450.0 1.00 ! from ST2 geometry LP OH2 450.0 0.80 ! ditto H H 0.0 1.6329931 ! from ST2 geometry (for SHAKE w/PARAM) HT OT 450.0 0.9572 ! from TIPS3P geometry HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) HA C 350.0 1.08 HA CT 300.0 1.08 HC NC2 405.0 1.00 HC NH1 405.0 0.98 HC NH3 405.0 1.04 OC S 400.0 1.43 OM OM 600.0 1.23! STRETCHING CONSTANT JUST A GUESS. S S 500.0 2.02 THETAS C C C 70.0 106.5! FROM B. R. GELIN THESIS WITH HARMONIC C C CH2E 65.0 126.5! PART OF F TERMS INCORPORATED. ATOMS C C CH3E 65.0 126.5! WITH EXTENDED H COMPENSATED FOR LACK C C CR1E 70.0 122.5! OF H ANGLES. C C CT 70.0 126.5 C C HA 40.0 120.0! AMIDE PARAMETERS FIT BY LEAST SQUARES C C NH1 65.0 109.0! TO N-METHYL ACETAMIDE VIBRATIONS. C C NP 65.0 112.5! MINIMIZATION OF N-METHYL ACETAMIDE. C C NR 65.0 112.5 C C OH1 65.0 119.0 C C O 65.0 119.0 ! FOR NETROPSIN CH1E C N 20.0 117.5 CH1E C NH1 20.0 117.5 CH1E C NH2 20.0 117.5 ! modified 20 06 03 CH1E C O 85.0 121.5 CH1E C OC 85.0 117.5 CH1E C OH1 85.0 120.0 CH2E C CR1E 70.0 121.5 CH2E C N 20.0 117.5 CH2E C NH1 20.0 117.5 CH2E C NH2 20.0 117.5 CH2E C NC2 20.0 117.5 ! FOR NETROPSIN CH2E C NR 60.0 116.0 CH2E C O 85.0 121.6 CH2E C OC 85.0 118.5 CH2E C OH1 85.0 120.0 CH3E C N 20.0 117.5 CH3E C NH1 20.0 117.5 CH3E C O 85.0 121.5 CR1E C CR1E 65.0 120.5 CR1E C NH1 65.0 110.5! USED ONLY IN HIS, NOT IT TRP CR1E C NP 65.0 122.5 CR1E C NR 65.0 122.5 CR1E C OH1 65.0 119.0 CT C N 20.0 117.5 CT C NH1 20.0 117.5 CT C NH2 20.0 117.5 CT C O 85.0 121.5 CT C OC 85.0 118.5 CT C OH1 85.0 120.0 HA C NH1 40.0 120.0 HA C NH2 40.0 120.0 HA C NR 40.0 120.0 HA C O 85.0 121.5 N C O 85.0 121.0 NC2 C NC2 70.0 120.0 NC2 C NH1 70.0 120.0 NH1 C NR 70.0 120.0 NH1 C O 65.0 121.0 NH2 C O 65.0 121.0 O C OH1 85.0 120.0 OC C OC 85.0 122.5 OS C CH1E 70.0 125.3! FROM PARDNA10 OS C CH2E 70.0 125.3! - " - OS C O 70.0 120.0! - " - C CH1E CH1E 70.0 110.0 C CH1E CH2E 70.0 109.5 C CH1E CH3E 70.0 106.5 C CH1E N 45.0 111.6 C CH1E NH1 45.0 111.6 C CH1E NH2 45.0 111.6 C CH1E NH3 45.0 111.6 CH1E CH1E CH2E 45.0 112.5 CH1E CH1E CH3E 45.0 111.0 CH1E CH1E NH1 50.0 110.0 CH1E CH1E NH2 50.0 109.5 CH1E CH1E NH3 50.0 107.5 CH1E CH1E OH1 50.0 104.5 CH2E CH1E CH3E 50.0 111.5 CH2E CH1E N 65.0 104.0 CH2E CH1E NH1 65.0 110.0 CH2E CH1E NH2 65.0 110.0 CH2E CH1E NH3 65.0 110.0 CH3E CH1E CH3E 50.0 111.0 CH3E CH1E NH1 65.0 108.5 CH3E CH1E NH2 65.0 109.5 CH3E CH1E NH3 65.0 109.5 CH3E CH1E OH1 60.0 110.5 C CH2E CH1E 70.0 112.5 C CH2E CH2E 70.0 113.0 C CH2E NH1 70.0 111.6 C CH2E NH2 70.0 111.6 C CH2E NH3 70.0 111.6 CH1E CH2E CH1E 45.0 117.0 CH1E CH2E CH2E 45.0 112.5 CH1E CH2E CH3E 45.0 113.0 CH1E CH2E OH1 45.0 111.0 CH3E CH2E OH1 45.0 111.0 CH1E CH2E S 50.0 112.5 CH1E CH2E SH1E 50.0 112.5 CH2E CH2E CH2E 45.0 110.0 CH2E CH2E CH3E 45.0 111.0 CH2E CH2E N 65.0 105.0 CH2E CH2E NH1 65.0 111.0 CH2E CH2E NH2 65.0 109.5 CH2E CH2E NH3 65.0 110.5 CH2E CH2E S 50.0 112.5 C CR1E C 90.0 126.5 C CR1E CH2E 90.0 122.0 C CR1E CR1E 90.0 119.0 C CR1E NH1 90.0 109.5 C CR1E NR 90.0 106.5 CR1E CR1E CR1E 90.0 120.5 NH1 CR1E NH1 70.0 109.0 NH1 CR1E NR 70.0 109.0 C CT CT 70.0 109.5 C CT HA 70.0 109.5 C CT N 70.0 111.6 C CT NH1 70.0 111.6 C CT NH2 70.0 111.6 C CT NH3 70.0 111.6 CT CT CT 45.0 111.00 CT CT HA 40.0 109.50 CT CT N 65.0 105.00 CT CT NC2 65.0 110.00 CT CT NH1 65.0 110.00 CT CT NH2 65.0 110.00 CT CT NH3 65.0 110.00 CT CT OH1 50.0 109.50 CT CT S 50.0 112.50 HA CT HA 40.0 109.5 HA CT N 50.0 109.5 HA CT NC2 50.0 109.5 HA CT NH1 50.0 109.5 HA CT NH3 50.0 109.5 HA CT OH1 50.0 109.5 HA CT S 40.0 109.5 FE CM OM 5.0 90.0! FROM KROEKER ET AL(1980) C N CH1E 80.0 120.0 C N CH2E 80.0 120.0 C N CT 80.0 120.0 CH1E N CH2E 60.0 110.0 CH1E N CH3E 60.0 110.0 CH2E N CH3E 60.0 109.5 CT N CT 60.0 110.0 C NC2 CT 80.0 120.0 C NC2 HC 35.0 120.0 CT NC2 HC 35.0 120.0 HC NC2 HC 40.0 120.0 C NH1 C 60.0 102.5 ! UNUSED (AND PROBABLY WRONG) C NH1 CH1E 77.5 120.0 C NH1 CH2E 77.5 120.0 C NH1 CH3E 77.5 120.0 C NH1 CR1E 60.0 108.0 C NH1 CT 80.0 120.0 C NH1 H 30.0 120.0 CH1E NH1 CH3E 60.0 120.0 CH1E NH1 H 35.0 120.0 CH2E NH1 CH3E 60.0 120.0 CH2E NH1 H 35.0 120.0 CH3E NH1 H 35.0 120.0 CR1E NH1 CR1E 65.0 110.0 CR1E NH1 H 35.0 120.0 CT NH1 H 35.0 120.0 C NH2 H 30.0 120.0 CH1E NH2 CH2E 60.0 120.0 CH1E NH2 H 35.0 120.0 CH2E NH2 H 35.0 120.0 CT NH2 H 35.0 120.0 H NH2 H 40.0 125.0 C NP C 70.0 102.5 C NP FE 50.0 128.0! FORCE CONSTANT FROM PARMFIX9 C NR C 70.0 102.5 C NR CR1E 70.0 109.5 CH3E NR CR1E 70.0 109.5 ! FOR NETROPSIN CH3E NR C 70.0 109.5 ! FOR NETROPSIN CR1E NR CR1E 65.0 110.0 CR1E NR FE 30.0 124.8! FORCE CONSTANT FROM PARMFIX9 CH1E NH3 HC 35.0 109.5 CH1E NH3 CH2E 35.0 109.5 CH2E NH3 HC 35.0 109.5 CT NH3 HC 35.0 109.5 HC NH3 HC 40.0 109.5 C OH1 H 50.0 109.5 CH1E OH1 H 35.0 109.5 CH2E OH1 H 35.0 109.5 CT OH1 H 35.0 109.5 H OH2 H 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S H OH2 LP 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S LP OH2 LP 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S FE OM OM 0.0 180.0! DUMMY PARAMETER FOR PATCH AND ANALYSIS. C OS CH3E 46.5 120.5! FROM PARDNA10 HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY CH2E S CH3E 50.0 99.5! FROM PARMFIX9, CHECK WITH IR CH2E S S 50.0 104.2 CT S CT 50.0 99.5! FORCE CONSTANTS FROM PARMFIX9 CT S S 50.0 104.2 OC S OC 85.0 109.5! FORCE CONSTANT JST A GUESS. NP FE CM 5.0 90.0 NP FE NP 50.0 90.0 NP FE NR 5.0 115.0 NP FE OM 5.0 90.0! JUST A GUESS FROM EXISTING FE CM DATA !NR FE CM 5.0 180.0 !NR FE OM 5.0 180.0! JUST A GUESS FROM EXISTING FE CM DATA PHI CH1E C N CH1E 10.0 2 180.0! PRO ISOM. BARRIER 20 KCAL/MOL. CH2E C N CH1E 10.0 2 180.0 CR1E C C CR1E 5.0 2 180.0! => TRP OOP. VIB 170CM 1 CR1E C C C 2.5 2 180.0! SEE BEHLEN ET AL JCP 75:5685 81 CR1E C C NH1 2.5 2 180.0 X C CH1E X 0.0 3 0.0! FROM GELIN THESIS AMIDES X C CH2E X 0.0 3 0.0! USING A SINGLE X C CR1E X 10.0 2 180.0! DIHEDRAL PER BOND RATHER X C CT X 0.0 3 0.0! THAN MULTIPLE TORSIONS. X C N X 8.2 2 180.0! ALKANE TORSION REDUCED TO X C NC2 X 8.2 2 180.0! 1.6 FROM 1.8 TO COINCIDE WITH X C NH1 X 8.2 2 180.0! THE EXPERIMENTAL BARRIER. X C NH2 X 8.2 2 180.0 X C OH1 X 1.8 2 180.0 X C OS X 1.8 2 180.0 ! INFERRED FROM C-OH1 X CH1E CH1E X 1.6 3 0.0 X CH1E CH2E X 1.6 3 0.0 X CH1E N X 0.3 3 0.0! FROM HAGLER ET AL TABULATION OF X CH1E NH1 X 0.3 3 0.0! EXP. DATA AND 6 31G CALC. X CH1E NH2 X 1.8 3 0.0! PROTONATED SECONDARY AMINE X CH1E NH3 X 0.6 3 0.0! 1/PROTON SO 3 FOR THE BOND X CH1E OH1 X 0.5 3 0.0! CHANGED TO ROUGHLY MEOH X CH2E CH2E X 1.6 3 0.0 X CH2E N X 0.3 3 0.0! SEE CH1E COMMENTS X CH2E NH1 X 0.3 3 0.0 X CH2E NH2 X 0.6 3 0.0 X CH2E NH3 X 0.6 3 0.0 X CH2E OH1 X 0.5 3 0.0 X CH2E S X 1.2 2 0.0 X CT CT X 1.6 3 0.0 X CT N X 0.3 3 0.0! SEE CH1E COMMENTS X CT NC2 X 0.3 3 0.0 X CT NH1 X 0.3 3 0.0 X CT NH2 X 0.6 3 0.0 X CT NH3 X 0.6 3 0.0 X CT OH1 X 0.5 3 0.0 X CT S X 1.2 2 0.0 X FE NR X 0.05 4 0.0 X FE CM X 0.05 4 0.0 X FE OM X 0.00 4 0.0 X S S X 4.0 2 0.0! FROM EXP. NMR BARRIER IMPHI C C CR1E CH2E 90.0 0 0.0! GIVE 220 CM 1 METHYL OOP FOR TOLUENE. C CR1E C CH2E 90.0 0 0.0! USED HERE FOR TRP CG OUT OF PLANE C CR1E CR1E CH2E 90.0 0 0.0! PHE, AND TYR CG OOP C CR1E NH1 CH2E 90.0 0 0.0! HIS CG RING OOP C NH1 CR1E CH2E 90.0 0 0.0! C CR1E CR1E OH1 150.0 0 0.0! GIVE 249 CM 1 PHENOL OH OOP. C H H NH2 45.0 0 0.0! PRIMARY AMIDES (ASN AND GLN) OOP C OC OC CH1E 100.0 0 0.0! CARBOXYL OUT OF PLANE. C OC OC CH2E 100.0 0 0.0! C X X C 25.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS C X X CH2E 90.0 0 0.0! FROM TOLUENE METHYL OOP. 217 CM 1 C X X CH3E 90.0 0 0.0 C X X CR1E 25.0 0 0.0 C X X H 75.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS C X X HA 75.0 0 0.0! C X X NH1 100.0 0 0.0! AMIDES FIT TO N METHYL ACETAMIDE. C X X O 100.0 0 0.0 C X X OC 100.0 0 0.0 C X X OH1 150.0 0 0.0! USED FOR TYR HYDROXYL OOP CH1E X X CH1E 55.0 0 35.26439! CALCULATED TO BE THE SAME AS THE 3 CH1E X X CH2E 55.0 0 35.26439! H CH1E X ANGLES WITH K=40 CH1E X X CH3E 55.0 0 35.26439 CR1E X X CR1E 25.0 0 0.0! EXTENDED ATOM VERSION OF BENZENE CR1E X X NH1 25.0 0 0.0! SAME AS ABOVE FOR LACK OF VALUES FE X X NP 20.0 0 0.0! FROM PARMFIX9 H X X O 45.0 0 0.0 N CH1E CH2E C 45.0 0 0.0! PROLINE NITROGENS N X X CH2E 45.0 0 0.0 N X X CT 45.0 0 0.0 NC2 X X CT 45.0 0 0.0 NC2 X X HC 45.0 0 0.0 NH1 X X CH1E 45.0 0 0.0 NH1 X X CH2E 45.0 0 0.0 NH1 X X CH3E 45.0 0 0.0 NH1 X X CT 45.0 0 0.0 NH1 X X H 45.0 0 0.0! AMIDES PROTON OOP NH1 X X NH1 25.0 0 0.0! NH1 X X NR 25.0 0 0.0 NH2 X X H 45.0 0 0.0 NR X X C 25.0 0 0.0 NR X X CR1E 25.0 0 0.0 NR X X CT 25.0 0 0.0 NR X X CH3E 25.0 0 0.0 ! FOR NETROPSIN ! NONBONDED NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSHIFT - CUTNB 8.0 CTOFNB 7.5 CTONNB 6.5 EPS 1.0 E14FAC 0.4 WMIN 1.5 ! ! Emin Rmin ! (kcal/mol) (A) H 0.0440 -0.0498 0.8000 HC 0.0440 -0.0498 0.6000 ! charged group. Reduced vdw radius HA 0.1000 -0.0450 1.4680 HT 0.0440 -0.0498 0.8000 !TIP3P water hydrogen, see NBFIX below ! C 1.65 -0.1200 2.100 1.65 -0.1 1.9 ! carbonyl carbon CH1E 1.35 -0.0486 2.365 1.35 -0.1 1.9 ! \ CH2E 1.77 -0.1142 2.235 1.77 -0.1 1.9 ! extended carbons CH3E 2.17 -0.1811 2.165 1.77 -0.1 1.9 ! / CR1E 1.35 -0.1200 2.100 1.35 -0.1 1.9 ! ring carbons C% 1.65 -0.0262 2.490 1.65 -0.1 1.9 ! includes CT and CM ! N* 1.1000 -0.2384 1.6000 ! includes N,NC2,NH1,NH2,NH3,NP,and NR ! O* 0.8400 -0.1591 1.6000 ! includes O, OH1, OM, and OS OC 2.1400 -0.6469 1.6000 OT 0.8400 -0.1591 1.6000 !TIP3P water oxygen, see NBFIX below OH2 0.0000 -0.0758 1.7398 !ST2 water oxygen ! LP 0.0000 -0.04598 0.2245 !ST2 lone pair FE 0.0100 0.000 0.6500 S* 0.3400 -0.0430 1.890 ! includes S and SH1E ! !CM 0.000000 -0.0262 2.150 ! CO 3-point model. !OM 0.000000 -0.1591 1.750 ! CO 3-point model. NBFIX ! Emin Rmin ! (kcal/mol) (A) ! ! We're gonna NBFIX the TIP3P water-water interactions ! here to make them more like Jorgensen's. The vdW parameters ! specified above will be in effect, therefore, for ONLY ! protein (read, protein OR nucleic acid)-water interactions. ! OT-OT is exactly Jorgensen's; HT interactions are added ! here. ! OT OT -0.152073 3.5365 ! TIPS3P VDW INTERACTION HT HT -0.04598 0.4490 HT OT -0.08363 1.9927 ! ! All protein-protein NBFIXes removed ! HBOND AEXP 4 REXP 6 HAEX 0 AAEX 0 NOACCEPTORS HBNOEXCLUSIONS ALL - CUTHB 0.5 CTOFHB 5.0 CTONHB 4.0 CUTHA 90.0 CTOFHA 90.0 CTONHA 90.0 ! N*+* N% -0.0 3.0 ! dummy parameters N*+* O* -0.00 2.9 ! OH* N% -0.00 2.85 OH* O* -0.00 2.75 END