AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Fri Nov 20 2009 - 10:02:57 CST

Ok, interesting. The "Unknown residue" message doesn't appear anymore while loading pdb...but I have now problem in saving amber params files:

Building topology.
Building atom parameters.
For atom: .R<ZN2 1311>.A<ZN 1> Could not find type: ZN
Parameter file was not saved.
>

20.11.09, 16:40, "FyD" <fyd_at_q4md-forcefieldtools.org>:

> Andrew,
>
> > Yes! It works now! The problem was that I've changed the atom name
> > rather than residue name in PDB and also residue name was also
> > shifted a bit left and was at last stage not ZN2 but N2.
>
> ok. This is a classical problem of recognition between your PDB & the
> FF libraries you load in LEaP.
>
> > I also wonder if it's ok to setup charge Zn2+ to a metal ion bound
> > to four amino acids or I should set up it as part of the protein then.
>
> Two approaches are possible:
> - The 1st one you consider Zn2+ not physically connected to your
> ligands & the total charge of the atom Zn is +2 (BTW do not forget to
> prepare a "frcmod" file for setting vdW parameters for your Zinc atom,
> I forgot to add this step @
> http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd).
> - The second one you derive charges for your Zn-complex were you will
> consider connections between Zinc & well-established ligands. In this
> case, the charge of Zn2+ should decreased to... some value ;-)
> I suggest you to use R.E.D.-III.3 and/or R.E.D. Server/R.E.D.-IV in
> the latter case.
>
> regards, Francois
>
>
>
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