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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Received on Fri Nov 20 2009 - 08:00:03 PST
