AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Aug 06 2009 - 10:29:39 CDT

I don't know of any such library. I would worry much more about the
difficult of getting accurate dihedral parameters than just charges.
Also see Feig's work on protonation changes for binding of protease
inhibitors.

On Aug 6, 2009, at 10:51 AM, "Oliver Kuhn" <O.Kuhn_at_gmx.net> wrote:

> Hi Amber Community,
>
> I want to do MMPBSA calculations on HIV protease - ligand complexes.
> At the moment, I am calculating with am1-bcc derived partial charges.
> All the publications I read have worked with gaussian98 and RESP and
> I would like to reproduce these works first before applying the
> method to unknown stuff.
> Calculating these parameters is heavily time-consuming.
>
> 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
>
> regards
> Oliver
>
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