Use VegaZZ to generate rotamers of your ligand, exhaustive search, random,
or Boltzmann weighted.
Then save as pdb or mol2 and use in Amber.
Best, use a flexible ligand docking program to generate your best pose
first.
Dean
On 6/15/11 9:41 AM, "abc def" <biotechabc.gmail.com> wrote:
>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
>>> > > > > > _______________________________________________
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>>
>>
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Received on Wed Jun 15 2011 - 19:00:03 PDT
