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

Amir Zeb zebamir85 at gmail.com
Mon Jan 9 01:54:20 CET 2017

Hello Tasneem,

Same like you, I'm pretty new to this field too. I don't know enough how to
calculate free energy in gromacs. I did only MM/PBSA for binding energy
I'll let you know if i get some thing relevant to your question.

All the best.


On Thu, Jan 5, 2017 at 10:28 PM, tasneem kausar <tasneemkausar12 at gmail.com>

> Dear all
> It is first time I am calculating free energy of protein and ligand. I am
> following the Justin's tutorial of methane in water free energy
> calculations. Though only van der waal lambda are defined so I have taken
> the mdp files from the alchemistry.org web page. Since the ligand and
> protein under my study have positive charges (one positive charge on ligand
> and tree positive charges on protein). So I have to add a CL ions in
> topology file to make a neutral sytem.
> Is it okay to use the system with ion for free energy calculation?
> If yes, What are change that can be made in mdp entry.
> Waiting for suggestions
> Thanks in Advance
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