[gmx-users] Volume of active site

[Ebert Maximilian]

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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