Actually just like rotamer library for side chain of protein. I want to
generate different conformational isomers of the ligand. And then from the
library, I want to screen the one which fits the best in the cavity of the
protein.
On Wed, Jun 15, 2011 at 8:07 PM, abc def <biotechabc.gmail.com> wrote:
> 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
>> > > > > > _______________________________________________
>> > > > > > AMBER mailing list
>> > > > > > AMBER.ambermd.org
>> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > >
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 15 2011 - 08:00:07 PDT
