Warren,
I also agree that this is a typo in the parm99.dat file and the below is
true where:
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.
SHOULD BE
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.
May I extend this caution to other typo's in the parm99.dat file!!!
I had found several and alerted Junmei to there presence and I guess that
this was not taken care of at the time.
Other typo's are:
X -CT-**ZC**-X 3 0.00 0.0 1. Junmei et
al, 1999
X -CT-**CZ**-X 3 0.00 0.0 1. Junmei et
al, 1999
**h1**-CT-CT-Cl 1 0.25 0.0 1. Junmei et
al, 1999
**H1**-CT-CT-Cl 1 0.25 0.0 1. Junmei et
al, 1999
HC-CT-CT-**f** 1 0.19 0.0 1. Junmei et
al, 1999
HC-CT-CT-**F** 1 0.19 0.0 1. Junmei et
al, 1999
**hC**-CT-CT-Cl 1 0.25 0.0 1. Junmei et
al, 1999
**HC**-CT-CT-Cl 1 0.25 0.0 1. Junmei et
al, 1999
HC-CT-CT-**br** 1 0.55 0.0 1. Junmei et
al, 1999
HC-CT-CT-**Br** 1 0.55 0.0 1. Junmei et
al, 1999
Craig A. Marhefka
Department of Pharmaceutical Sciences
University of Tennessee
847 Monroe Ave. Suite 327
Memphis, TN 38163
e-mail: cmarhefka_at_utmem.edu
Lab: (901)448-7814
Office: (901)448-7530
Fax: (901)448-6828
___________________________________________
"The mind is not a vessel to be filled,
but a fire to be lighted"
Author Unknown
___________________________________________
> 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 Fri Jan 26 2001 - 12:19:45 PST
