[gmx-users] Volume of active site

[Raj D]

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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>