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

tasneem kausar tasneemkausar12 at gmail.com
Sat Jan 7 05:27:25 CET 2017

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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