[gmx-users] Volume of active site

[Gaurav Goel]

CASTp might prove useful.
http://sts.bioe.uic.edu/castp/

-g


On Thu, Jun 4, 2015 at 8:31 PM, Raj D <gromacs.for.f at gmail.com> wrote:

> 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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-- 
Gaurav Goel, PhD
Assistant Professor
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016
India