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
> > > _______________________________________________
> > > 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
> _______________________________________________
> 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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- application/x-sh attachment: scan.sh
Received on Tue Sep 27 2011 - 05:30:03 PDT
