[gmx-users] Volume of active site

[Raj D]

Thanks Dr Erick .
On Jun 4, 2015 6:43 PM, "Erik Marklund" <erik.marklund at chem.ox.ac.uk> wrote:

> 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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