[gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

mm/pbsa calculates binding energy. I have used that.

On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebamir85 at gmail.com> wrote:

> hello
> you may use mm/pbsa compiled with gromacs to calculate free energy
> all the best
>
> On Jan 7, 2017 1:27 PM, "tasneem kausar" <tasneemkausar12 at gmail.com>
> wrote:
>
> > Dear gromacs users
> >
> > It is first time I am trying to perform free energy calculation of
> protein
> > and drug complex. I am following Justin' s tutorial of mehtane in water.
> > That calculation are performed on a neutral system. If the ligand
> molecule
> > has charge what are the provisions that could be taken into account.
> > I have performed my MD simulation using force field gromos54a7. And Now I
> > am trying to go onward using free energy calculations. Since the free
> > energy calculations are performed on ambed99ldn, opls and charmm force
> > fields (as I know from the articles). Is it okay to use gromos54a7 ff for
> > free energy calculations.
> >
> > Kindly tell me
> >
> > Thanks in Advance
> > --
> > 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.
>