Re: [AMBER] To calculate TI using soft-core potential or not

From: Daniel Mermelstein <>
Date: Tue, 5 Dec 2017 13:54:40 -0800

Hi Yang,

You don't have to use softcore. The only thing you have to be careful with
is, assuming you're doing this calculation as part of a thermodynamic
cycle, that all of your vdw parameters changes either all use softcore or
all don't use softcore.



On Tue, Dec 5, 2017 at 12:35 AM, Yang Jinpeng <> wrote:

> Dear proffessor:
> I want to calculate deltaG between complex AL and compelx BL
> ,where L represents ligand. There are the same number of atoms between AL
> and BL, while several atoms of A are different from B. Besides, the
> geometric structure of AL is slightly different from BL. Is it necessary to
> calculate deltaG between AL and BL using soft-core potential? Does deltaG
> make a big difference using soft-core potential or not?
> Thanks in advance. Your any reply will help me a lot.
> All the regards,
> Yang Jinpeng
> _______________________________________________
> AMBER mailing list

Daniel J. Mermelstein, Ph.D candidate
McCammon & Walker Groups
Department of Chemistry & Biochemistry
University of California, San Diego
AMBER mailing list
Received on Tue Dec 05 2017 - 14:00:01 PST
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