[gmx-users] Volume of active site

[Erik Marklund]

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> 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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