AMBER Archive (2003)

Subject: Re: AMBER: PMF ethane example: Can someone correct the INPUT? Thanks.

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 03 2003 - 10:38:56 CDT

On Tue, Sep 02, 2003, Christophe L M J Verlinde wrote:
>
> PLEASE, CAN SOMEONE GIVE US A CLUE ON HOW TO CORRECT THE INPUT FOR
> THIS SIMPLE PMF CALCULATION.

Just a note: the lack of response is not an indication of disinterest in the
problem, but reflects more the fact that none of the current Amber developers
have ever used this feature of gibbs. I hope that someone on the list will
be able to respond, but if not, you will probably have to study the code
yourself.

Unless someone can step up to help, it is almost certain that we will have to
drop gibbs from future Amber releases, since there is no real way to provide
effective user support. We are in the process of extending the free energy
capabilities of sander to make up for this.

..good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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