AMBER Archive (2004)

Subject: Re: AMBER: FEP along a reaction coordinate in sander

From: Masataka Nagaoka (mnagaoka_at_is.nagoya-u.ac.jp)
Date: Wed Dec 01 2004 - 06:05:01 CST

                                             Dr. Masataka Nagaoka
                            _/_/_/_/_/ Professor
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           _/ Graduate School of Information Science,
  _/_/_/_/_/ Nagoya University, Chikusa-ku, Nagoya 464-8601, JAPAN
                  E-mail: mnagaoka_at_is.nagoya-u.ac.jp
                 http: //frontier.ncube.human.nagoya-u.ac.jp/
                Tel&Fax: +81-52-789-5623

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Dear Dr. Tomasz Borowski,

I am Prof. Masataka Nagaoka at Nagoya University, JAPAN.
Such a research as you are now interested in, is one of current projects of our
group. I am sending some recent results which have been publised in Journals.
If you are interested in them, please e-mail for further discussion.

Best regards,
Masataka
================================================================================
>Dear All,
>
>I'd like to do FEP calculations along (ab-initio)
>reaction path for a small organic system in water.
>(to get the solvation contribution to the activation
>free energy). Let's say I have the coordinates for
>several points along this path with corresponding
>RESP charges. Can I use sander to do TI along this
>path? I assume I can perturb the charges and VDW
>parms, but can I change the geometry when changing
>lambda?
>
>I'll be greatful for any suggestions,
>
>best regards,
>
>Tomasz Borowski
>
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