[gmx-users] Volume of active site

[RINU KHATTRI]

hello gromacs users
its working i have calculated the volume and density of active site
residues (in one group) but it gives value like time in ps volume
density if i want to calculate the per residue wise change  in volume
and density is there any way.
thanks in advance

On Mon, Jun 1, 2015 at 10:03 PM, Raj D <gromacs.for.f at gmail.com> wrote:
> 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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