Jason
Thanks for your reply. I am taking the parameters from another work. I have
one more doubt regarding this. When I look into Amber parm file, I see in
case of dihedrals with multiple periodicities, PN sometimes go from -3 -2 1
and sometimes -1 -2 3. I understand the meaning of the negative sign in
Amber. But if the authors have mentioned V1 V2 V3 do I automatically assume
that the PN values would be -1 -2 and 3?
On Thu, Feb 21, 2013 at 6:52 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Feb 21, 2013 at 2:13 AM, DEBOSTUTI GHOSHDASTIDAR <
> debostutighosh.gmail.com> wrote:
>
> > Dear Amber Users...
> >
> > I am using OPLS-AA force field parameters for running simulations for
> ionic
> > liquid using Amber. I have some doubts regarding the preparation of the
> > dihedral part of the frc file using these OPLS parameters. I would use an
> > example to explain the doubt.
> >
> > >From the paper JCTC (vol 5, 2009, pp 1038) I get the following
> information
> > for a particular dihedral
> >
> > dihedral V1
> > V2 V3
> > NA-CA-CS-CS -1.788 0.756
> > -0.288
> >
> > When I use these values in the amber frc file,
> >
> > PK = V1/2 V2/2 V3/2
> >
> > PN = -3, -2, 1
> >
> > Is that right?
> >
> > Now I have the following queries:
> >
> > 1) does a negative value of Vn imply a phase shift of 180deg?How do I
> > determine the phase shift?
> >
>
> Yes, the phase shift is 180 degrees. The Vn is the multiplicative constant
> in front of a cosine term, and cos(x+180) = -cos(x)
>
> 2) Why are all the PK values in amber parm file positive and some in this
> > format negative?
> >
>
> You can get the same effect by either setting the phase shift to 180
> directly or by making the PK value negative. Most Amber force fields
> always set PK positive, although I think some GLYCAM parameters use
> negative PKs (and perhaps OPLS parameters do as well).
>
>
> > 3) How do I determine the IDIV factor. Should I determine them by
> > understanding how many torsions are there around that bond and divide PK
> by
> > that value? Or do the authors already take that into consideration and
> give
> > value for a single torsion (so in that case my IDIV factor will be one in
> > all cases)
> >
>
> I guess I'm not understanding what data you have. If you are determining
> the parameters yourself, you will need to take care of the dividing factor.
> The typical convention adopted by Amber is to provide a non-unity dividing
> factor only for generic dihedrals (e.g., X -CT-CT-X ). For specific
> dihedrals (i.e., where all 4 atoms are specified directly and there are no
> wild cards), we typically set the dividing factor to 1 and make sure that
> the barrier height is properly adjusted for the superposition of the
> expected number of dihedrals.
>
> If you're taking the parameters from somewhere, you should assume that they
> have either set IDIVF correctly or that IDIVF should be 1 and PK is
> appropriately set (unless they specifically state otherwise).
>
> If you are in doubt, it never hurts to validate.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti Ghosh Dastidar
PhD Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Thu Feb 21 2013 - 06:00:02 PST
