[gmx-users] Volume of active site

[Raj D]

Thanks Dr Ebert ...looks very useful site for my purpose and I try it
tomorrow when I get to the lab.
Regards,
Raja
On Jun 1, 2015 9:52 PM, "Ebert Maximilian" <m.ebert at umontreal.ca> wrote:

> Hi Raja,
>
> you could also give 3V a try: http://3vee.molmovdb.org
>
> Cheers,
> Max
>
> On Jun 1, 2015, at 11:12 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk
> <mailto:erik.marklund at chem.ox.ac.uk>> wrote:
>
> Dear Raja,
>
> Depending on how you define that volume, you may achieve what you want
> through clever use of g_sas -tv (gmx sas nowadays).
>
> Kind regards,
> Erik
>
> On 1 Jun 2015, at 15:19, Raj D <gromacs.for.f at gmail.com<mailto:
> gromacs.for.f at gmail.com>> wrote:
>
> Dear user,
> I have completed a set of MD simulations of mutants and wild type of a
> protein complexed with its substrate in its active site , I have inferred
> that the active sites of all mutant enzymes have gone enlarged relative to
> wild type which is  consistent with our kinetic study of the mutants, the
> Km values are so high for all mutant enzymes and I would like quantify the
> volume of the active site comprising a set of 17 active site residues ..Is
> there any direct or indirect tool in gromacs to compute the volume like
> that ? Or any free tools available .
> Regards,
> Raja
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