are you trying to sample different rotamers in your minimization? or are you
trying to restrain to the initial rotamer? If you want to restrain them, you
can do this using the NMR restraints. There are many examples in the
archives. The data is specified in the disang file.
On Wed, Jun 15, 2011 at 10:11 AM, abc def <biotechabc.gmail.com> wrote:
> Hi,
>
> I have gone through the basic ones. By rotatable bonds I mean that
> supposedly in a molecule / protein ligand a C is connected to four
> different
> heavy atoms and that may be connected further to any atoms either by
> single/double/triple bond. So the bond say C-C is single..and hence can be
> easily rotated unmlike the bond say C=O. So I want to restrict the
> minimization of all those bonds involving C in sp3 hybridized form, for
> example.
>
> Similarly there may be more such bonds in the ligand molecule. How can this
> be done? Or can you please direct me to the tutorial in which such a
> minimization has been employed?
>
> Thanks,
>
> Pooja Khurana
>
> On Wed, Jun 15, 2011 at 4:02 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > what exactly do you mean by minimization of the rotatable bonds?
> > have you worked through the tutorials on the amber web site?
> > On Wed, Jun 15, 2011 at 6:01 AM, Pooja Khurana <btpooja.yahoo.in> wrote:
> >
> > > Hi everyone,
> > >
> > > Is it possible to do the restraint minimization of the rotatable bonds
> in
> > a
> > > molecule?
> > > And if yes then how it can be done? Actually I am a beginner, so need
> > some
> > > help to implement the same.
> > >
> > > Hoping for an early reply.
> > >
> > > Thanks in anticipation,
> > >
> > > Pooja Khurana
> > > B.E. Biotechnology
> > > India
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jun 15 2011 - 07:30:05 PDT
