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

[Amir Zeb]

well
if you are confident of your simulation you may definitly go ahead with
this ff
otherwise you will have to change the ff for simulation too
i think this is not rational to simulate the system with one ff and then
change the ff for free energy calculations

good luck

On Jan 7, 2017 2:01 PM, "tasneem kausar" <tasneemkausar12 at gmail.com> wrote:

> Thanks Amir Zeb for your reply
> I have read in literature about the FEPsetup to parametrize the complex
> file (protein+drug) for simulation. This setup builds files based on amber.
> Since I have previously used 54a7ff to simulate the protein and drug and
> topology files were generated from ATB in gromos54a7 format. Since I didn't
> find free energy calculation of protein and ligand with this force field.
> Thats why I was confused to proceed further using the same.
>
> On Sat, Jan 7, 2017 at 10:07 AM, 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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