AMBER Archive (2009)

Subject: Re: [AMBER] parameters for HIV protease inhibitors

• Previous message: subarna thakur: "[AMBER] query regarding fes cluster"
• In reply to: Oliver Kuhn: "[AMBER] parameters for HIV protease inhibitors"
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Dear Oliver,

> The question is: Does anybody know a ressource with readily prepared
> parameters (gaussian98/gammes + RESP) for amber99SB or amber03,
> namely for
> amprenavir indinavir nelfinavir saquinavir atazanavir darunavir
> lopinavir ritonavir tipranavir

Yes getting charges for these structures can take some time. That
being said, you could use the building block approach based on
(multiple orientations, multiple conformations) and multiple
molecules. In this case, you are going to save cpu time (during the
geometry optimization step). You could also imagine compute the
charges for your whole molecule list in a single R.E.D. or R.E.D.
Server job. By modifying one keyword in R.E.D. Server you will
generate charges for the amber99SB or amber03 FFs.

regards, Francois

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• Previous message: subarna thakur: "[AMBER] query regarding fes cluster"
• In reply to: Oliver Kuhn: "[AMBER] parameters for HIV protease inhibitors"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]