X-PLOR Parameter Files

The parameter files contain the parameters which correspond to the various bonds and angles listed in the PSF file above. The files contain parameters which are appropriate for different types of molecules and molecular environments (proteins, solvent, etc.). The units for the angle energy constants is kcal/mol/rad². An example parameter file follows below (param19.pro for proteins):

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 ++++
!! 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


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
...

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
...

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
...

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
...

{* nonbonding parameter section *}
{* ============================ *}
!! for use with:
!! NBXMOD=5  ATOM CDIEL SHIFT vswitch 
!!    CUTNB=8.0  CTOFNB=7.5  CTONNB=6.5  EPS=1.0  E14FAC=0.4  WMIN=1.5
!!

 !                  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
...

set echo=true end