AMBER Archive (2009)

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

From: Oliver Kuhn (oak.amber_at_web.de)
Date: Tue Aug 11 2009 - 09:57:24 CDT

> -----Ursprüngliche Nachricht-----
> Von: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
> Gesendet: 06.08.09 17:31:40
> An: AMBER Mailing List <amber_at_ambermd.org>
> Betreff: Re: [AMBER] parameters for HIV protease inhibitors

> 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.

Thank you Carlos. I'm actually trying to reproduce the monoprotonated cases of this work.
I have found prep and frcmod files for saquinavir and indinavir from
http://www.pharmacy.manchester.ac.uk/bryce/amber
but the inhibitors come in parts and I couldn't yet figure out how to use them.

 I'm going to do charge calculations using R.E.D (gamess/RESP).
For the dihedrals I have read something in Thomas Steinbrecher's Dissertation. Reads as follows:

(Derive all other forcefield params first.)
Then do two calculations:
Calculate energy profile for the rotation around the single bond with QM and fixed dihedral angles in constant portions.
Then calculate the energy profile with same dihedral angles with the molecular mechanics force field setting the params of the dihedral angle to zero.
Subtract both energy profiles form each other and choose params for the dihedral ange to fit the energy profiles difference.

Do you know any literature or implementation on this method or dihedral param derivation in general?

Another thing, I tried to answer this post "query regarding resp" and instead of my post, these post appeared on the list:
Osmar Norberto de Souza Resposta automática de Ausęncia temporária: [AMBER] query regarding resp
Paul Mortenson Out of Office AutoReply: [AMBER] query regarding resp
Laura VanZant Out of Office AutoReply: [AMBER] query regarding resp

So, somebody must be on holiday - I don't get it. Maybe you can help me with that.

best regards
Oliver

>
> 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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