AMBER Archive (2009)

Subject: AW: [AMBER] zinc coordination of benzimidazole

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Fri Jun 12 2009 - 01:13:19 CDT

Hello Urszula,
thanks for your answer. I forgot to tell you, that other calculations with
Zn-enzyme-ligand complexes run well (ligands = imidazole, peptide. So I don't
think, that the problem is the zinc ion, it's only a problem of
benzimidazole.
Has anyone an idea?

Thanks a lot! Susanne

-----Ursprüngliche Nachricht-----
Von: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]Im
Auftrag von Urszula Uciechowska
Gesendet: 11 June 2009 10:50
An: AMBER Mailing List
Betreff: Re: [AMBER] zinc coordination of benzimidazole

I would try Pang approach for your zinc ( it treats the zinc ion as
thetrahedron-shaped divalent cation with dummy atoms).

I hope that will help

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg

----- Ursprüngliche Nachricht -----
Von: "Aust, Susanne" <saust_at_ipb-halle.de>
Datum: Donnerstag, Juni 11, 2009 9:11
Betreff: [AMBER] zinc coordination of benzimidazole
An: "Amber (E-Mail)" <amber_at_ambermd.org>

> > Dear Amber-users,
> > I have a problem with the coordination of benzimidazole derivatives
> on zinc
> > during Amber minimization an md calculations. I work with Amber10.
> > At first I generate the parameters for benzimidazole with
> antechamber and
> > bcc charges. Everything is ok. Then I prepare my enzyme-benzimidazole
> > complex with xleap, for zinc2+ I have a extra library. I add ions
> and use a
> > TIP3P waterbox. Everything is o.k. and I generate prmtop and inpcrd.
> Then I
> > minimize with sander
> > 1. only the waterbox and the ions,
> > 2. only the ligand,
> > 3. the whole system.
> > When I check now the structure (please see the pdb-file
> > c2k_bzim_correct_min.pdb), the benzimidaole isn't coordinated on the
> zinc
> > atom (distance: 3.8 A).
> > At my first trail I used by mistake a chemical wrong structure of
> > benzimidazole. Here the ligand is after the minimization coordinated.
> > I try to calculate different enzymes with benzimidazole-derivatives,
> but
> > everytime the same happens. The zinc-atom leaves the benzimidazole,
> but the
> > other amino acids are correct coordinated on zinc (they go with the
> zinc).
> > I don't see the failure in my preparation of the complex.
> > Do you know problems with benzimidazole?
> > Thanks a lot for your help. When I forgot any detail, which you must
> have,
> > please let me know!
> >
> > Susanne
> >
> <<c2k_bzim_correct.pdb>> <<bzim_correct.frcmod>>
> <<bzim_correct.mol2>>
> <<bzim_correct.prepin>> <<ZNA.lib>> <<frcmod.zna>>
> <<c2k_bzim_correct_min.pdb>>
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