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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Received on Wed Jun 15 2011 - 07:30:04 PDT
