Thanks Carlos for your quick reply. I don't want to generate the side chain
rotamers of protein. I want to sample different rotamers of a ligand
molecule. So is there any way in doing so in amber?
On Wed, Jun 15, 2011 at 8:02 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> no. what you are looking for is a side chain optimization program. This is
> global optimization. Amber will do local optimization. Perhaps others on
> this list will know of good ways to find the best side chain rotamers.
>
>
> On Wed, Jun 15, 2011 at 10:26 AM, abc def <biotechabc.gmail.com> wrote:
>
> > Ya basically I want to sample different rotamers for finding the best
> > suitable one for docking purpose. So for that what I need to generate
> > different rotamers. Will the NMR restraint work for it?
> >
> >
> > Thanks
> >
> > Pooja Khurana
> >
> >
> > On Wed, Jun 15, 2011 at 7:46 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > 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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Received on Wed Jun 15 2011 - 08:00:06 PDT
