AMBER Archive (2007)

Subject: AMBER: Integrating the alpha-helix bias correction into ff94

From: Andrew Borgert (borg0109_at_umn.edu)
Date: Mon Aug 06 2007 - 14:18:58 CDT

Amber users,
    I am running into problems with AMBER biasing my MD runs toward
alpha-helices and I would like to apply the correction developed by
Simmerling et. all. Unfortunately the correction was written for ff99,
while I am forced to use ff94 due to compatibility issues with
Glycam_04. I know that in ff99, the correction would overwrite several
dihedral terms in parm99.dat, however these terms do not exist in
parm94.dat (there are of course similar terms, but none that exactly
match those in the correction). Here is the correction:

from Simmerling, Strockbine, Roitberg, JACS 124:11258, 2002. Modifies
parm99.
MASS

BOND

ANGL

DIHEDRAL
N -CT-C -N 1 0.700 180.000 -1.
N -CT-C -N 1 1.100 180.000 2.
C -N -CT-C 1 1.000 0.000 1.

NONB

and here are the similar (but not exactly the same) terms found in
parm94.dat

C -N -CT-C 1 2.000 180.000 2.
N -CT-C -N 1 0.400 180.000 -4.
N -CT-C -N 1 1.350 180.000 -2.
N -CT-C -N 1 0.750 180.000 1.

I assume that if I loaded both parm94 and the correction in Xleap, none
of the N -CT-C -N terms would be overwritten, since none of them are
exactly the same as those in the correction. So then, if I wish to
apply the correction, do I need to delete the N -CT-C -N terms from
parm94 and input the correction terms?

Thanks,
    Andrew Borgert
    University of Minnesota
    Biophysical Science and Medical Physics
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