AMBER Archive (2004)

Subject: Re: Re: AMBER: about FEP

From: Thomas Steinbrecher (
Date: Wed Nov 03 2004 - 02:07:51 CST

Hi Xiao,

> Thanks for your reply.I want to calculate differences in complexation free energy of two ligands binding to the same
> protein and mutate one ligand into another in the presence of both protein and aqueous solution to calculate
> the (delta delta G) using TI method.
> I'm not sure in the commands in leap to make the correct information for the perturbation since the two ligand changes
> a bit.

I did some calculations like that a while ago. Could you send your ligand
*.lib file which contains the perturbation information?



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