[gmx-users] Fwd: clustering based on side-chain conformations

[Justin Lemkul]

On 4/2/13 4:58 AM, anu chandra wrote:
> Dear Justin,
>
> Thanks for your immediate reply.
>
> Is it possible to do clustering based on side-chain RMSF in gromacs?
>

Not that I'm aware of.

> What about dihedral angle order parameters in gromacs?. Does it provide any
> information about what I want to know?
>

You can probably get some useful information, but I don't know how to calculate 
such quantities in Gromacs, and any clustering you would do would have to be 
external to Gromacs.

-Justin

> Thanking you once again
>
> regards
> Anu
>
>
> On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>> On Mon, Apr 1, 2013 at 4:52 AM, anu chandra <anu80125 at gmail.com> wrote:
>>
>>> Dear amber users,
>>>
>>> I am working with protein-ligand interaction. The protein shows high
>> degree
>>> of side-chain conformational changes and minimal backbone conformational
>>> changes during ligand binding. In order to capture these side chain
>>> flexibility, as a initial step,  I would like to do clustering based on
>> the
>>> side-chain flexibility (i.e. categorise different areas in protein based
>> on
>>> the degree of side chain flexibility). Is there a way to do such a
>>> calculation in Gromacs?. Can any one suggested me a way to proceed with
>>> this sort of analysis?
>>>
>>>
>> g_cluster does RMSD-based clustering. That's not "flexibility" per se, but
>> might be informative. If you do fitting based on side chains (which might
>> be difficult, since side chains flop around a lot), that's about as close
>> to achieving what you're after as I can think of using standard Gromacs
>> programs.
>>
>> -Justin
>>
>> --
>>
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540)
>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================