Hi Jason,
Thank you for the information on dihedral parameters. I want
to know, how can we generate the dihedral potential energy surface using
amber11 and GAFF. Can you suggest any tutorial if it exists.
with regards,
Chidambar Kulkarni
On Tue, Sep 27, 2011 at 6:38 AM, Jason Swails <jason.swails.gmail.com>wrote:
> You could perform a minimized scan using both an appropriate QM method and
> the force field without your dihedral parameter, then fit your parameters
> to
> the difference. I've taken that approach to parametrizing the dihedral
> term
> between connected benzene rings in the past with some success.
>
> Of course this won't work too well if you're missing too many parameters.
>
> HTH,
> Jason
>
> On Mon, Sep 26, 2011 at 5:09 PM, kirtana S <skirtana4.gmail.com> wrote:
>
> > I am using a inorganic nanocluster protected with organic interface.
> > Can anyone tell me how to know the parameters for dihedral ,
> >
> > IPT JPT KPT LPT IDIVF PK PHASE PN
> >
> > Please tell me how we derive the parameters for IDIVF is 1 PK is 0 .
> > How should I go for the other parameters in this section .
> >
> > Thanks
> > Kirtana
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chidambar k
Int.PhD
JNCASR
Bangalore
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Received on Mon Sep 26 2011 - 21:00:03 PDT
