remark - parameter file PARAM19 - remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 set echo=false end !! - 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 ++++ !! 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 bond C C 450.0 1.38! B. R. GELIN THESIS AMIDE AND DIPEPTIDES bond C CH1E 405.0 1.52! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT bond C CH2E 405.0 1.52! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED bond C CH3E 405.0 1.52 bond C CR1E 450.0 1.38 bond C CT 405.0 1.53 bond C N 471.0 1.33 bond C NC2 400.0 1.33! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE bond C NH1 471.0 1.33 bond C NH2 471.0 1.33 bond C NP 471.0 1.33 bond C NR 471.0 1.33 bond C O 580.0 1.23 bond C OC 580.0 1.23! FORCE DECREASE AND LENGTH INCREASE FROM C O bond C OH1 450.0 1.38! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) bond C OS 292.0 1.43! FROM DEP NORMAL MODE FIT bond CH1E CH1E 225.0 1.53 bond CH1E CH2E 225.0 1.52 bond CH1E CH3E 225.0 1.52 bond CH1E N 422.0 1.45 bond CH1E NH1 422.0 1.45 bond CH1E NH2 422.0 1.45 bond CH1E NH3 422.0 1.45 bond CH1E OH1 400.0 1.42! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) bond CH2E CH2E 225.0 1.52 bond CH2E CH3E 225.0 1.54 bond CH2E CR1E 250.0 1.45! FROM WARSHEL AND KARPLUS 1972 JACS 96:5612 bond CH2E N 422.0 1.45 bond CH2E NH1 422.0 1.45 bond CH2E NH2 422.0 1.45 bond CH2E NH3 422.0 1.45 bond CH2E OH1 400.0 1.42 bond CH2E S 450.0 1.81! FROM PARMFIX9 bond CH2E SH1E 450.0 1.81 bond CH3E NH1 422.0 1.49 bond CH3E NR 422.0 1.49 ! FOR NETROPSIN bond CH3E S 450.0 1.77! FROM PARMFIX9 bond CH3E OS 292.0 1.38! FROM DEP NORMAL MODE FIT bond CM OM 1115.0 1.128! FROM CAUGHEY ET AL(1978),CARBON MONOXIDE bond CR1E CR1E 450.0 1.38 bond CR1E NH1 450.0 1.305 bond CR1E NR 450.0 1.305 bond CT CT 200.0 1.53 bond CT N 422.0 1.45 bond CT NC2 422.0 1.45 bond CT NH1 422.0 1.45 bond CT NH2 422.0 1.45 bond CT NH3 422.0 1.45 bond CT OH1 400.0 1.42 bond CT S 450.0 1.81 !bond FE CM 258.0 1.79! FROM KROEKER ET AL(JCP:72:4846) !bond FE NP 500.0 2.09 !bond FE NR 65.0 1.98! FROM NAGAI ET AL(1980) !bond FE OM 250.0 1.8! JUST A GUESS. bond H NH1 405.0 0.98! GELIN AND IR STRETCH 3200 CM 1 bond H NH2 405.0 0.98 bond H OH1 450.0 0.96! FROM IR STRETCH 3400 CM 1 bond HA C 350.0 1.08 bond HA CT 300.0 1.08 bond HC NC2 405.0 1.00 bond HC NH1 405.0 0.98 bond HC NH3 405.0 1.04 bond OC S 400.0 1.43 bond OM OM 600.0 1.23! STRETCHING CONSTANT JUST A GUESS. bond S S 500.0 2.02 angle C C C 70.0 106.5! FROM B. R. GELIN THESIS WITH HARMONIC angle C C CH2E 65.0 126.5! PART OF F TERMS INCORPORATED. ATOMS angle C C CH3E 65.0 126.5! WITH EXTENDED H COMPENSATED FOR LACK angle C C CR1E 70.0 122.5! OF H ANGLES. angle C C CT 70.0 126.5 angle C C HA 40.0 120.0! AMIDE PARAMETERS FIT BY LEAST SQUARES angle C C NH1 65.0 109.0! TO N-METHYL ACETAMIDE VIBRATIONS. angle C C NP 65.0 112.5! MINIMIZATION OF N-METHYL ACETAMIDE. angle C C NR 65.0 112.5 angle C C OH1 65.0 119.0 angle C C O 65.0 119.0 ! FOR NETROPSIN angle CH1E C N 20.0 117.5 angle CH1E C NH1 20.0 117.5 angle CH1E C O 85.0 121.5 angle CH1E C OC 85.0 117.5 angle CH1E C OH1 85.0 120.0 angle CH2E C CR1E 70.0 121.5 angle CH2E C N 20.0 117.5 angle CH2E C NH1 20.0 117.5 angle CH2E C NH2 20.0 117.5 angle CH2E C NC2 20.0 117.5 ! FOR NETROPSIN angle CH2E C NR 60.0 116.0 angle CH2E C O 85.0 121.6 angle CH2E C OC 85.0 118.5 angle CH2E C OH1 85.0 120.0 angle CH3E C N 20.0 117.5 angle CH3E C NH1 20.0 117.5 angle CH3E C O 85.0 121.5 angle CR1E C CR1E 65.0 120.5 angle CR1E C NH1 65.0 110.5! USED ONLY IN HIS, NOT IT TRP angle CR1E C NP 65.0 122.5 angle CR1E C NR 65.0 122.5 angle CR1E C OH1 65.0 119.0 angle CT C N 20.0 117.5 angle CT C NH1 20.0 117.5 angle CT C NH2 20.0 117.5 angle CT C O 85.0 121.5 angle CT C OC 85.0 118.5 angle CT C OH1 85.0 120.0 angle HA C NH1 40.0 120.0 angle HA C NH2 40.0 120.0 angle HA C NR 40.0 120.0 angle HA C O 85.0 121.5 angle N C O 85.0 121.0 angle NC2 C NC2 70.0 120.0 angle NC2 C NH1 70.0 120.0 angle NH1 C NR 70.0 120.0 angle NH1 C O 65.0 121.0 angle NH2 C O 65.0 121.0 angle O C OH1 85.0 120.0 angle OC C OC 85.0 122.5 angle OS C CH1E 70.0 125.3! FROM PARDNA10 angle OS C CH2E 70.0 125.3! - " - angle OS C O 70.0 120.0! - " - angle C CH1E CH1E 70.0 110.0 angle C CH1E CH2E 70.0 109.5 angle C CH1E CH3E 70.0 106.5 angle C CH1E N 45.0 111.6 angle C CH1E NH1 45.0 111.6 angle C CH1E NH2 45.0 111.6 angle C CH1E NH3 45.0 111.6 angle CH1E CH1E CH2E 45.0 112.5 angle CH1E CH1E CH3E 45.0 111.0 angle CH1E CH1E NH1 50.0 110.0 angle CH1E CH1E NH2 50.0 109.5 angle CH1E CH1E NH3 50.0 107.5 angle CH1E CH1E OH1 50.0 104.5 angle CH2E CH1E CH3E 50.0 111.5 angle CH2E CH1E N 65.0 104.0 angle CH2E CH1E NH1 65.0 110.0 angle CH2E CH1E NH2 65.0 110.0 angle CH2E CH1E NH3 65.0 110.0 angle CH3E CH1E CH3E 50.0 111.0 angle CH3E CH1E NH1 65.0 108.5 angle CH3E CH1E NH2 65.0 109.5 angle CH3E CH1E NH3 65.0 109.5 angle CH3E CH1E OH1 60.0 110.5 angle C CH2E CH1E 70.0 112.5 angle C CH2E CH2E 70.0 113.0 angle C CH2E NH1 70.0 111.6 angle C CH2E NH2 70.0 111.6 angle C CH2E NH3 70.0 111.6 angle CH1E CH2E CH1E 45.0 117.0 angle CH1E CH2E CH2E 45.0 112.5 angle CH1E CH2E CH3E 45.0 113.0 angle CH1E CH2E OH1 45.0 111.0 angle CH3E CH2E OH1 45.0 111.0 angle CH1E CH2E S 50.0 112.5 angle CH1E CH2E SH1E 50.0 112.5 angle CH2E CH2E CH2E 45.0 110.0 angle CH2E CH2E CH3E 45.0 111.0 angle CH2E CH2E N 65.0 105.0 angle CH2E CH2E NH1 65.0 111.0 angle CH2E CH2E NH2 65.0 109.5 angle CH2E CH2E NH3 65.0 110.5 angle CH2E CH2E S 50.0 112.5 angle C CR1E C 90.0 126.5 angle C CR1E CH2E 90.0 122.0 angle C CR1E CR1E 90.0 119.0 angle C CR1E NH1 90.0 109.5 angle C CR1E NR 90.0 106.5 angle CR1E CR1E CR1E 90.0 120.5 angle NH1 CR1E NH1 70.0 109.0 angle NH1 CR1E NR 70.0 109.0 angle C CT CT 70.0 109.5 angle C CT HA 70.0 109.5 angle C CT N 70.0 111.6 angle C CT NH1 70.0 111.6 angle C CT NH2 70.0 111.6 angle C CT NH3 70.0 111.6 angle CT CT CT 45.0 111.00 angle CT CT HA 40.0 109.50 angle CT CT N 65.0 105.00 angle CT CT NC2 65.0 110.00 angle CT CT NH1 65.0 110.00 angle CT CT NH2 65.0 110.00 angle CT CT NH3 65.0 110.00 angle CT CT OH1 50.0 109.50 angle CT CT S 50.0 112.50 angle HA CT HA 40.0 109.5 angle HA CT N 50.0 109.5 angle HA CT NC2 50.0 109.5 angle HA CT NH1 50.0 109.5 angle HA CT NH3 50.0 109.5 angle HA CT OH1 50.0 109.5 angle HA CT S 40.0 109.5 !angle FE CM OM 5.0 90.0! FROM KROEKER ET AL(1980) angle C N CH1E 80.0 120.0 angle C N CH2E 80.0 120.0 angle C N CT 80.0 120.0 angle CH1E N CH2E 60.0 110.0 angle CH1E N CH3E 60.0 110.0 angle CH2E N CH3E 60.0 109.5 angle CT N CT 60.0 110.0 angle C NC2 CT 80.0 120.0 angle C NC2 HC 35.0 120.0 angle CT NC2 HC 35.0 120.0 angle HC NC2 HC 40.0 120.0 angle C NH1 C 60.0 102.5 ! UNUSED (AND PROBABLY WRONG) angle C NH1 CH1E 77.5 120.0 angle C NH1 CH2E 77.5 120.0 angle C NH1 CH3E 77.5 120.0 angle C NH1 CR1E 60.0 108.0 angle C NH1 CT 80.0 120.0 angle C NH1 H 30.0 120.0 angle CH1E NH1 CH3E 60.0 120.0 angle CH1E NH1 H 35.0 120.0 angle CH2E NH1 CH3E 60.0 120.0 angle CH2E NH1 H 35.0 120.0 angle CH3E NH1 H 35.0 120.0 angle CR1E NH1 CR1E 65.0 110.0 angle CR1E NH1 H 35.0 120.0 angle CT NH1 H 35.0 120.0 angle C NH2 H 30.0 120.0 angle CH1E NH2 CH2E 60.0 120.0 angle CH1E NH2 H 35.0 120.0 angle CH2E NH2 H 35.0 120.0 angle CT NH2 H 35.0 120.0 angle H NH2 H 40.0 125.0 angle C NP C 70.0 102.5 !angle C NP FE 50.0 128.0! FORCE CONSTANT FROM PARMFIX9 angle C NR C 70.0 102.5 angle C NR CR1E 70.0 109.5 angle CH3E NR CR1E 70.0 109.5 ! FOR NETROPSIN angle CH3E NR C 70.0 109.5 ! FOR NETROPSIN angle CR1E NR CR1E 65.0 110.0 !angle CR1E NR FE 30.0 124.8! FORCE CONSTANT FROM PARMFIX9 angle CH1E NH3 HC 35.0 109.5 angle CH1E NH3 CH2E 35.0 109.5 angle CH2E NH3 HC 35.0 109.5 angle CT NH3 HC 35.0 109.5 angle HC NH3 HC 40.0 109.5 angle C OH1 H 50.0 109.5 angle CH1E OH1 H 35.0 109.5 angle CH2E OH1 H 35.0 109.5 angle CT OH1 H 35.0 109.5 !angle FE OM OM 0.0 180.0! DUMMY PARAMETER FOR PATCH AND ANALYSIS. angle C OS CH3E 46.5 120.5! FROM PARDNA10 angle CH2E S CH3E 50.0 99.5! FROM PARMFIX9, CHECK WITH IR angle CH2E S S 50.0 104.2 angle CT S CT 50.0 99.5! FORCE CONSTANTS FROM PARMFIX9 angle CT S S 50.0 104.2 angle OC S OC 85.0 109.5! FORCE CONSTANT JST A GUESS. !angle NP FE CM 5.0 90.0 !angle NP FE NP 50.0 90.0 !angle NP FE NR 5.0 115.0 !angle NP FE OM 5.0 90.0! JUST A GUESS FROM EXISTING FE CM DATA !angle NR FE CM 5.0 180.0 !angle NR FE OM 5.0 180.0! JUST A GUESS FROM EXISTING FE CM DATA dihe CH1E C N CH1E 10.0 2 180.0! PRO ISOM. BARRIER 20 KCAL/MOL. dihe CH2E C N CH1E 10.0 2 180.0 dihe CR1E C C CR1E 5.0 2 180.0! => TRP OOP. VIB 170CM 1 dihe CR1E C C C 2.5 2 180.0! SEE BEHLEN ET AL JCP 75:5685 81 dihe CR1E C C NH1 2.5 2 180.0 dihe X C CH1E X 0.0 3 0.0! FROM GELIN THESIS AMIDES dihe X C CH2E X 0.0 3 0.0! USING A SINGLE dihe X C CR1E X 10.0 2 180.0! DIHEDRAL PER BOND RATHER dihe X C CT X 0.0 3 0.0! THAN MULTIPLE TORSIONS. dihe X C N X 8.2 2 180.0! ALKANE TORSION REDUCED TO dihe X C NC2 X 8.2 2 180.0! 1.6 FROM 1.8 TO COINCIDE WITH dihe X C NH1 X 8.2 2 180.0! THE EXPERIMENTAL BARRIER. dihe X C NH2 X 8.2 2 180.0 dihe X C OH1 X 1.8 2 180.0 dihe X C OS X 1.8 2 180.0 ! INFERRED FROM C-OH1 dihe X CH1E CH1E X 1.6 3 0.0 dihe X CH1E CH2E X 1.6 3 0.0 dihe X CH1E N X 0.3 3 0.0! FROM HAGLER ET AL TABULATION OF dihe X CH1E NH1 X 0.3 3 0.0! EXP. DATA AND 6 31G CALC. dihe X CH1E NH2 X 1.8 3 0.0! PROTONATED SECONDARY AMINE dihe X CH1E NH3 X 0.6 3 0.0! 1/PROTON SO 3 FOR THE BOND dihe X CH1E OH1 X 0.5 3 0.0! CHANGED TO ROUGHLY MEOH dihe X CH2E CH2E X 1.6 3 0.0 dihe X CH2E N X 0.3 3 0.0! SEE CH1E COMMENTS dihe X CH2E NH1 X 0.3 3 0.0 dihe X CH2E NH2 X 0.6 3 0.0 dihe X CH2E NH3 X 0.6 3 0.0 dihe X CH2E OH1 X 0.5 3 0.0 dihe X CH2E S X 1.2 2 0.0 dihe X CT CT X 1.6 3 0.0 dihe X CT N X 0.3 3 0.0! SEE CH1E COMMENTS dihe X CT NC2 X 0.3 3 0.0 dihe X CT NH1 X 0.3 3 0.0 dihe X CT NH2 X 0.6 3 0.0 dihe X CT NH3 X 0.6 3 0.0 dihe X CT OH1 X 0.5 3 0.0 dihe X CT S X 1.2 2 0.0 !dihe X FE NR X 0.05 4 0.0 !dihe X FE CM X 0.05 4 0.0 !dihe X FE OM X 0.00 4 0.0 dihe X S S X 4.0 2 0.0! FROM EXP.R BARRI impr C C CR1E CH2E 90.0 0 0.0!GIVE 220 CM 1 METHYL OOP FOR TOLUENE. impr C CR1E C CH2E 90.0 0 0.0!USED HERE FOR TRP CG OUT OF PLANE impr C CR1E CR1E CH2E 90.0 0 0.0! PHE, AND TYR CG OOP impr C CR1E NH1 CH2E 90.0 0 0.0! HIS CG RING OOP impr C NH1 CR1E CH2E 90.0 0 0.0! impr C CR1E CR1E OH1 150.0 0 0.0! GIVE 249 CM 1 PHENOL OH OOP. impr C H H NH2 45.0 0 0.0! PRIMARY AMIDES (ASN AND GLN) OOP impr C OC OC CH1E 100.0 0 0.0! CARBOXYL OUT OF PLANE. impr C OC OC CH2E 100.0 0 0.0! impr C X X C 25.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS impr C X X CH2E 90.0 0 0.0! FROM TOLUENE METHYL OOP. 217 CM 1 impr C X X CH3E 90.0 0 0.0 impr C X X CR1E 25.0 0 0.0 impr C X X H 75.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS impr C X X HA 75.0 0 0.0! impr C X X NH1 100.0 0 0.0! AMIDES FIT TO N METHYL ACETAMIDE. impr C X X O 100.0 0 0.0 impr C X X OC 100.0 0 0.0 impr C X X OH1 150.0 0 0.0! USED FOR TYR HYDROXYL OOP impr CH1E X X CH1E 55.0 0 35.26439! CALCULATED TO BE THE SAME AS THE 3 impr CH1E X X CH2E 55.0 0 35.26439! H CH1E X ANGLES WITH K=40 impr CH1E X X CH3E 55.0 0 35.26439 impr CR1E X X CR1E 25.0 0 0.0! EXTENDED ATOM VERSION OF BENZENE impr CR1E X X NH1 25.0 0 0.0! SAME AS ABOVE FOR LACK OF VALUES !impr FE X X NP 20.0 0 0.0! FROM PARMFIX9 impr H X X O 45.0 0 0.0 impr N CH1E CH2E C 45.0 0 0.0! PROLINE NITROGENS impr N X X CH2E 45.0 0 0.0 impr N X X CT 45.0 0 0.0 impr NC2 X X CT 45.0 0 0.0 impr NC2 X X HC 45.0 0 0.0 impr NH1 X X CH1E 45.0 0 0.0 impr NH1 X X CH2E 45.0 0 0.0 impr NH1 X X CH3E 45.0 0 0.0 impr NH1 X X CT 45.0 0 0.0 impr NH1 X X H 45.0 0 0.0! AMIDES PROTON OOP impr NH1 X X NH1 25.0 0 0.0! impr NH1 X X NR 25.0 0 0.0 impr NH2 X X H 45.0 0 0.0 impr NR X X C 25.0 0 0.0 impr NR X X CR1E 25.0 0 0.0 impr NR X X CT 25.0 0 0.0 impr NR X X CH3E 25.0 0 0.0 ! FOR NETROPSIN {* nonbonding parameter section *} {* ============================ *} ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) ! --------------------------------------- NONBonded H 0.0498 1.4254 0.0498 1.4254 NONBonded HA 0.0450 2.6157 0.0450 2.6157 !- charged group. NONBonded HC 0.0498 1.0691 0.0498 1.0691 ! Reduced vdw radius ! NONBonded C 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded CH1E 0.0486 4.2140 0.1000 3.3854 ! \ NONBonded CH2E 0.1142 3.9823 0.1000 3.3854 ! extended carbons NONBonded CH3E 0.1811 3.8576 0.1000 3.3854 ! / !! NONBonded CM 0.0262 4.4367 0.1000 3.3854 NONBonded CR1E 0.1200 3.7418 0.1000 3.3854 ! ring carbons !! NONBonded CT 0.0262 4.4367 0.1000 3.3854 ! NONBonded N 0.2384 2.8509 0.2384 2.8509 NONBonded NC2 0.2384 2.8509 0.2384 2.8509 NONBonded NH1 0.2384 2.8509 0.2384 2.8509 NONBonded NH2 0.2384 2.8509 0.2384 2.8509 NONBonded NH3 0.2384 2.8509 0.2384 2.8509 NONBonded NP 0.2384 2.8509 0.2384 2.8509 NONBonded NR 0.2384 2.8509 0.2384 2.8509 ! NONBonded O 0.1591 2.8509 0.1591 2.8509 NONBonded OC 0.6469 2.8509 0.6469 2.8509 NONBonded OH1 0.1591 2.8509 0.1591 2.8509 !! NONBonded OM 0.1591 2.8509 0.1591 2.8509 NONBonded OS 0.1591 2.8509 0.1591 2.8509 ! NONBonded S 0.0430 3.3676 0.0430 3.3676 NONBonded SH1E 0.0430 3.3676 0.0430 3.3676 ! !! NONBONDED FE 0.0000 1.1582 0.0000 1.1582 set echo=true end