AMBER Archive (2009)

Subject: [AMBER] zinc coordination of benzimidazole

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Thu Jun 11 2009 - 02:09:59 CDT

> 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>>






  • application/octet-stream attachment: ZNA.lib



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