AMBER Archive (2009)

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

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Mon Nov 23 2009 - 06:35:55 CST

Hm, frcmod should be prepared by antechamber. Now we got antechamber error here:

$ antechamber -i zn2.pdb -fi pdb -o zn2.prepin -fo prepi -c bcc -s 2

Running: /amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 0; net charge: 0

Running: /amber10/bin/mopac.sh
Error: unable to find mopac charges in mopac.out

This is zn2.pdb, maybe there is something wrong with PDB file:

HETATM 1666 ZN ZN2 1 -34.053 -24.945 -27.759 1.00 27.33 ZN
END

20.11.09, 18:47, "FyD" <fyd_at_q4md-forcefieldtools.org>:

> Quoting Andrew Voronkov :
>
> > 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.A Could not find type: ZN
> > Parameter file was not saved.
>
> See updated http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd
> & BTW do not forget to prepare a "frcmod" file for setting vdW
> parameters for your Zinc atom, I forgot to add this step
>
> F.
>
>
> > 20.11.09, 16:40, "FyD" :
> >
> >> 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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> >>
> >>
> >
> > _______________________________________________
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> >
> >
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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