Thanks a lot Jason, both for the script as well as the advice.
with regards,
Chidambar
On Tue, Sep 27, 2011 at 5:31 PM, Jason Swails <jason.swails.gmail.com>wrote:
> I attached a script I wrote to do it. What it does is use the NMR
> restraint
> facility and just change the location of the restraint until it scans the
> whole dihedral.
>
> I suggest learning what the script is doing (it's written in bash, so it's
> fairly straight-forward to understand) rather than just blindly using it.
>
> HTH,
> Jason
>
> On Mon, Sep 26, 2011 at 11:51 PM, Chidambar Kulkarni
> <chidkul007.gmail.com>wrote:
>
> > 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
> > > > _______________________________________________
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> > > > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Chidambar k
> > Int.PhD
> > JNCASR
> > Bangalore
> > _______________________________________________
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Chidambar k
Int.PhD
JNCASR
Bangalore
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Received on Tue Sep 27 2011 - 09:30:05 PDT
