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

Amir Zeb zebamir85 at gmail.com
Sat Jan 7 05:30:17 CET 2017

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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