Download User Manual for EGO VIII - Max-Planck

A.1. INPUT FILES
63
...
24 !NNB
45
44
208
224
43
223
97
222
96
236
95
235
210
234
209
328
0 !NGRP
0
0
5
0
0
7
0
...
222
0
0
...
A.1.4 X-PLOR Parameter Files
The parameter les contain the parameters which correspond to the various bonds and angles
listed in the PSF le above. The les contain parameters which are appropriate for dierent
types
of
molecules
and molecular environments (proteins, solvent, etc.). The units for the angle energy constants is kcal=mol=rad2 . An example parameter le follows below (param19.pro for proteins):
remark
remark
remark
remark
- 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
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
bond C
bond C
...
C
CH1E
CH2E
angle C
angle C
angle C
...
C
C
C
dihe CH1E C
dihe CH2E C
dihe CR1E C
...
Release 2.0
450.0
405.0
405.0
C
CH2E
CH3E
N
N
C
1.38!
1.52!
1.52!
B. R. GELIN THESIS AMIDE AND DIPEPTIDES
EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT
ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED
70.0 106.5!
65.0 126.5!
65.0 126.5!
CH1E 10.0
CH1E 10.0
CR1E 5.0
2
2
2
FROM B. R. GELIN THESIS WITH HARMONIC
PART OF F TERMS INCORPORATED. ATOMS
WITH EXTENDED H COMPENSATED FOR LACK
180.0! PRO ISOM. BARRIER 20 KCAL/MOL.
180.0
180.0! => TRP OOP. VIB 170CM 1
April 13, 2000