Re: AMBER: how to check metal ion bonding ?

From: Bill Ross <>
Date: Tue, 13 Apr 2004 14:34:52 -0700 (PDT)

> I am trying to add Zinc to Cystine. I have followed the same procedure as
> in Plastocyanin tutorial in the manual. Leap went fine without any error
> messages. Before I start with minimization I want to make sure that all
> the bonds with the Zinc are properly formed.
> I have tried using Xleap, Sybyl, spdbv programs but the zinc ion and its
> bonds were not shown.

You have to actually add the bonds to the model yourself, either by
drawing them with the mouse in the editor in xleap, or via the command
interface. (Or by creating a new residue template that includes them
by default, again by drawing or commanding, or by manual spec in a
prepin file.)

Graphical programs will often show bonds where they are plausible
(by the program's own residue templates and/or distance), but xleap's
'unit editor' will only show bonds that are in the amber model (hence
in the prmtop) itself. To have "amber bonds" show reliably in another
molecular view program that loads pdb format, the CONECT records would
have to be included in pdb files generated by leap's savepdb cmd and/or
the ambpdb program. As far as I know, this is not currently the case.

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Received on Tue Apr 13 2004 - 22:53:00 PDT
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