[gmx-users] g_lie restraints, neutral ??

Mikko Hellgren Mikko.Hellgren at ki.se
Wed Sep 13 16:09:55 CEST 2006

Hi MD people! 
Some questions about g_lie.....
My purpose is to score different ligands and get a rough estimation of
the free energy of binding between free and bound state of the ligands
and protein of interest.

1. When I run my ligands in water without the protein, should
I add counterions (Cl and Na) to make the system neutral. 

2. Should I put any restraints on the ligand in the simulation without
the protein?  

3. When I run my ligand bound to the protein. Should I put restraints
any restrains on protein or ligand My initial thought would be to put
on c-alpha of the protein and let the rest of the system be "free". 
Thank you for any suggestions or comments, by the way I have checked all
previous threads with g_lie or lie without any to me clear suggestions
about these questions.

Take care,
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