The Simmerling, Strockbine, Roitberg ref is NOT ff99SB, it was an earlier
version but we made several more improvements in ff99SB (especially
to glycine).
here are the key phi/psi ff99SB parameters:
C -N -CT-C 1 0.00 0.0 -4. four
amplitudes and Simmerling's ff99SB mod:Hornak et al, Proteins
65:712-725 2006
C -N -CT-C 1 0.42 0.0 -3. phases for
GLY/phi Simmerling's ff99SB mod
C -N -CT-C 1 0.27 0.0 -2.
Simmerling's ff99SB mod
C -N -CT-C 1 0.00 0.0 1.
Simmerling's ff99SB mod
N -CT-C -N 1 0.00 0.0 -4. four
amplitudes and Simmerling's ff99SB mod
N -CT-C -N 1 0.55 180.0 -3. phases for
GLY/psi Simmerling's ff99SB mod
N -CT-C -N 1 1.58 180.0 -2.
Simmerling's ff99SB mod
N -CT-C -N 1 0.45 180.0 1.
Simmerling's ff99SB mod
CT-CT-N -C 1 0.00 0.0 -4. four amplitudes and
CT-CT-N -C 1 0.40 0.0 -3. phases for
ALA/CB-phi* Simmerling's ff99SB mod
CT-CT-N -C 1 2.00 0.0 -2. (it's not
really phi) Simmerling's ff99SB mod
CT-CT-N -C 1 2.00 0.0 1.
Simmerling's ff99SB mod
CT-CT-C -N 1 0.00 0.0 -4. four
amplitudes and Simmerling's ff99SB mod
CT-CT-C -N 1 0.40 0.0 -3. phases for
ALA/CB-psi* Simmerling's ff99SB mod
CT-CT-C -N 1 0.20 0.0 -2. (it's not
really psi) Simmerling's ff99SB mod
CT-CT-C -N 1 0.20 0.0 1.
Simmerling's ff99SB mod
I would suggest taking these and copying them into into ff94.
but I have not extensively tested that. One
possible issue is that ff99 also changed some side chain torsions and
all of our validation was done with that. I've thought of doing energy
correlations for ff99SB and "ff94SB" on lots of conformations of peptides,
but haven't actually done it.
carlos
On 8/6/07, Andrew Borgert <borg0109.umn.edu> wrote:
> 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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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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Received on Wed Aug 08 2007 - 06:07:27 PDT
