jim caldwell wrote:
> Those are multi term dihedral functions. I.e. the
> potential is a sum of term in sin n theta, sin 2n theta
> etc. The expansion is explained in the manual.
>
> jim
>
Quite correct, but you missed my point. Notice that there are two multiterm
dihedrals for the *same* dihedral! But read on...
The comments may contain the answer: In both parm94.dat and parm96.dat, we
have the following entries, which are missing in parm99.dat.
parm94.dat and parm96.dat
CT-CT-N -C 1 0.50 180.0 -4.
CT-CT-N -C 1 0.15 180.0 -3.
CT-CT-N -C 1 0.53 0.0 1.
parm99.dat:
C -CT-N -C 1 0.50 180.0 -4.
C -CT-N -C 1 0.15 180.0 -3.
C -CT-N -C 1 0.53 0.0 1.
This looks like a TYPE. "CT-CT-N -C " got changed to a "C -CT-N -C " in
parm99.dat, and we ended up with duplicated and missing (wildcard fallback)
peptide dihedrals! This looks to me like a major typo, one that may cast a
shadow on any simulations previously run with parm99.dat. Jim or others,
please confirm. Is this a real error?
- Warren
Warren DeLano wrote:
> I noticed a puzzling set of parameters for amide torsions in the
> parm99.dat file (directly from the Amber web site, Jun-mei Wang's work -
> lines 534-538)
>
> C -N -CT-C 1 0.850 180.000 -2.
> C -N -CT-C 1 0.800 0.000 1.
> C -CT-N -C 1 0.50 180.0 -4.
> phi,psi,parm94
> C -CT-N -C 1 0.15 180.0 -3.
> phi,psi,parm94
> C -CT-N -C 1 0.53 0.0 1.
> phi,psi,parm94
--
mailto:warren_at_sunesis-pharma.com
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
3696 Haven Ave., Suite C
Redwood City, CA 94063
(650)-562-3106 fax: (650)-556-8824
Received on Thu Jan 25 2001 - 17:06:04 PST
