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

[tasneem kausar]

Thanks again

That is it what I was asking. I have seen the topology files of t4-lysozyme
with its ligand. It was provided by alchemistry.org tutorial. Can I change
the topology accordingly.
Another thing is the charge on the ligand molecule. How this will be
handled in free energy calculations.

Waiting for your suggestion

On Sat, Jan 7, 2017 at 10:35 AM, Amir Zeb <zebamir85 at gmail.com> wrote:

> 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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