how to set up free energy perturbation

From: Mao Xiang <>
Date: Sun 04 Jun 2000 18:23:40 +0900

    Here is a simple question about how to do free energy perturbation.
I want to mutate a amino acid to another one, and I have set the, PERT.type and PERT.charge. And I also build a file contain
the properties of the pert.type atom, and read in using loadamberparams,
and then I saveamberparmpert the topology and coordinate of my protein.
But when I run gibbs, it says that I attempt to run GIBBS with a
non-perturbation parm (prmtop) file. So I think there must be some wrong
with my setup. I wish you can give me some explaination step by step
about how to set up the perturbation. Thank you very much.


| Xiang Mao |
| Lab of Molecular Regulation for Microbial Secondary Metabolism |
| Shanghai institute of Plant Physiology, Academia Sinica |
| 300 Fenglin Road, Shanghai, China, 200032 |
| Tel: +86-21-64042090-4791 |
| Fax: +86-21-64042385 |
Received on Sun Jun 04 2000 - 02:23:40 PDT
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