📄 alanin.params
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angle CT CT S 50.0 112.50angle HA CT HA 40.0 109.5angle HA CT N 50.0 109.5angle HA CT NC2 50.0 109.5angle HA CT NH1 50.0 109.5angle HA CT NH3 50.0 109.5angle HA CT OH1 50.0 109.5angle HA CT S 40.0 109.5!angle FE CM OM 5.0 90.0! FROM KROEKER ET AL(1980)angle C N CH1E 80.0 120.0angle C N CH2E 80.0 120.0angle C N CT 80.0 120.0angle CH1E N CH2E 60.0 110.0angle CH1E N CH3E 60.0 110.0angle CH2E N CH3E 60.0 109.5angle CT N CT 60.0 110.0angle C NC2 CT 80.0 120.0angle C NC2 HC 35.0 120.0angle CT NC2 HC 35.0 120.0angle HC NC2 HC 40.0 120.0angle C NH1 C 60.0 102.5 ! UNUSED (AND PROBABLY WRONG)angle C NH1 CH1E 77.5 120.0angle C NH1 CH2E 77.5 120.0angle C NH1 CH3E 77.5 120.0angle C NH1 CR1E 60.0 108.0angle C NH1 CT 80.0 120.0angle C NH1 H 30.0 120.0angle CH1E NH1 CH3E 60.0 120.0angle CH1E NH1 H 35.0 120.0angle CH2E NH1 CH3E 60.0 120.0angle CH2E NH1 H 35.0 120.0angle CH3E NH1 H 35.0 120.0angle CR1E NH1 CR1E 65.0 110.0angle CR1E NH1 H 35.0 120.0angle CT NH1 H 35.0 120.0angle C NH2 H 30.0 120.0angle CH1E NH2 CH2E 60.0 120.0angle CH1E NH2 H 35.0 120.0angle CH2E NH2 H 35.0 120.0angle CT NH2 H 35.0 120.0angle H NH2 H 40.0 125.0angle C NP C 70.0 102.5!angle C NP FE 50.0 128.0! FORCE CONSTANT FROM PARMFIX9angle C NR C 70.0 102.5angle C NR CR1E 70.0 109.5angle CH3E NR CR1E 70.0 109.5 ! FOR NETROPSINangle CH3E NR C 70.0 109.5 ! FOR NETROPSINangle CR1E NR CR1E 65.0 110.0!angle CR1E NR FE 30.0 124.8! FORCE CONSTANT FROM PARMFIX9angle CH1E NH3 HC 35.0 109.5angle CH1E NH3 CH2E 35.0 109.5angle CH2E NH3 HC 35.0 109.5angle CT NH3 HC 35.0 109.5angle HC NH3 HC 40.0 109.5angle C OH1 H 50.0 109.5angle CH1E OH1 H 35.0 109.5angle CH2E OH1 H 35.0 109.5angle 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 PARDNA10angle CH2E S CH3E 50.0 99.5! FROM PARMFIX9, CHECK WITH IRangle CH2E S S 50.0 104.2angle CT S CT 50.0 99.5! FORCE CONSTANTS FROM PARMFIX9angle CT S S 50.0 104.2angle 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 DATAdihe CH1E C N CH1E 10.0 2 180.0! PRO ISOM. BARRIER 20 KCAL/MOL.dihe CH2E C N CH1E 10.0 2 180.0dihe CR1E C C CR1E 5.0 2 180.0! => TRP OOP. VIB 170CM 1dihe CR1E C C C 2.5 2 180.0! SEE BEHLEN ET AL JCP 75:5685 81dihe CR1E C C NH1 2.5 2 180.0dihe X C CH1E X 0.0 3 0.0! FROM GELIN THESIS AMIDESdihe X C CH2E X 0.0 3 0.0! USING A SINGLEdihe X C CR1E X 10.0 2 180.0! DIHEDRAL PER BOND RATHERdihe 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 TOdihe X C NC2 X 8.2 2 180.0! 1.6 FROM 1.8 TO COINCIDE WITHdihe X C NH1 X 8.2 2 180.0! THE EXPERIMENTAL BARRIER.dihe X C NH2 X 8.2 2 180.0dihe X C OH1 X 1.8 2 180.0dihe X C OS X 1.8 2 180.0 ! INFERRED FROM C-OH1dihe X CH1E CH1E X 1.6 3 0.0dihe X CH1E CH2E X 1.6 3 0.0dihe X CH1E N X 0.3 3 0.0! FROM HAGLER ET AL TABULATION OFdihe 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 AMINEdihe X CH1E NH3 X 0.6 3 0.0! 1/PROTON SO 3 FOR THE BONDdihe X CH1E OH1 X 0.5 3 0.0! CHANGED TO ROUGHLY MEOHdihe X CH2E CH2E X 1.6 3 0.0dihe X CH2E N X 0.3 3 0.0! SEE CH1E COMMENTSdihe X CH2E NH1 X 0.3 3 0.0dihe X CH2E NH2 X 0.6 3 0.0dihe X CH2E NH3 X 0.6 3 0.0dihe X CH2E OH1 X 0.5 3 0.0dihe X CH2E S X 1.2 2 0.0dihe X CT CT X 1.6 3 0.0dihe X CT N X 0.3 3 0.0! SEE CH1E COMMENTSdihe X CT NC2 X 0.3 3 0.0dihe X CT NH1 X 0.3 3 0.0dihe X CT NH2 X 0.6 3 0.0dihe X CT NH3 X 0.6 3 0.0dihe X CT OH1 X 0.5 3 0.0dihe 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 0.0dihe X S S X 4.0 2 0.0! FROM EXP.R BARRIimpr 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 PLANEimpr C CR1E CR1E CH2E 90.0 0 0.0! PHE, AND TYR CG OOPimpr C CR1E NH1 CH2E 90.0 0 0.0! HIS CG RING OOPimpr 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) OOPimpr 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 ANALYSISimpr C X X CH2E 90.0 0 0.0! FROM TOLUENE METHYL OOP. 217 CM 1impr C X X CH3E 90.0 0 0.0impr C X X CR1E 25.0 0 0.0impr C X X H 75.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSISimpr 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 0.0impr C X X OC 100.0 0 0.0impr C X X OH1 150.0 0 0.0! USED FOR TYR HYDROXYL OOPimpr CH1E X X CH1E 55.0 0 35.26439! CALCULATED TO BE THE SAME AS THE 3impr CH1E X X CH2E 55.0 0 35.26439! H CH1E X ANGLES WITH K=40impr CH1E X X CH3E 55.0 0 35.26439impr CR1E X X CR1E 25.0 0 0.0! EXTENDED ATOM VERSION OF BENZENEimpr 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 PARMFIX9impr H X X O 45.0 0 0.0impr N CH1E CH2E C 45.0 0 0.0! PROLINE NITROGENSimpr N X X CH2E 45.0 0 0.0impr N X X CT 45.0 0 0.0impr NC2 X X CT 45.0 0 0.0impr NC2 X X HC 45.0 0 0.0impr NH1 X X CH1E 45.0 0 0.0impr NH1 X X CH2E 45.0 0 0.0impr NH1 X X CH3E 45.0 0 0.0impr NH1 X X CT 45.0 0 0.0impr NH1 X X H 45.0 0 0.0! AMIDES PROTON OOPimpr NH1 X X NH1 25.0 0 0.0! impr NH1 X X NR 25.0 0 0.0impr NH2 X X H 45.0 0 0.0impr NR X X C 25.0 0 0.0impr NR X X CR1E 25.0 0 0.0impr NR X X CT 25.0 0 0.0impr 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 1.1582set echo=true end⌨️ 快捷键说明
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