[gmx-users] Volume of active site

[Raj D]

Thanks Dr Gaurav , I will give a try in there .
Regards,
Raja
On Jun 5, 2015 11:02 AM, "Gaurav Goel" <gauravgoeluta at gmail.com> wrote:

> 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
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