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

[Amir Zeb]

alright
why do you care of forcefield in terms of free energy calculations?
do you have literature in reference for your protein simulated with a
specific ff?

On Jan 7, 2017 1:38 PM, "tasneem kausar" <tasneemkausar12 at gmail.com> wrote:

> 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
> > > --
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