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 OC   C    OH1     85.0 120.0 !guess from o-c-oh1
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

impr NH3  HC   HC   HC    55.0    0 35.26439 ! guess for NH3 (MN, IP)

{* 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


 !                  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
