[gmx-users] Volume of active site

[Erik Marklund]

Dear Raja,

It seems that what you need to calculate is the volume of the convex hull for the active site, which to my knowledge is not something gromacs is capable of at the moment.

Kind regards,
Erik

> On 3 Jun 2015, at 07:28, Raj D <gromacs.for.f at gmail.com> wrote:
> 
> Dear Erik,
> As per your suggestion I have tried gmx sasa -tv  option to get the
> volume   of the active site with help of a defined set of residues (17
> residues) as defined in the index file. But for all systems, mutants and
> wild type enzymes have similar profile of volume throughout the simulation
> time of 10ns and all volume shows up 6 nm3 as center point but
> visualization has shown widening of active site in the simulation. Is it
> the right approach to get the volume of the defined cavity or something
> like may I have to remove the bound substrate from the trajectory or some
> other thing I have to take care of while using the tool... I am just wonder
> what you had mentioned as clever use of the tool gmx sasa ? Could you
> please little more explicit in the usage of the tool for volume prediction .
> Regards,
> Raja
> On Jun 1, 2015 8:42 PM, "Erik Marklund" <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> 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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