Re: AMBER: Formatting Questions

From: Kara Di Giorgio <>
Date: Tue, 22 Feb 2005 13:48:46 -0800

My ligand is a rather rigid structure. I'm pretty sure I can get it to
go through antechamber to assign bond types/angles, etc if I remove the
Ni atom. Looking at the crown ether tutorial, I could then import the
Ni information (positional coordinates) along with the ligand into
xLeap and combine them there. I've always been planning on entering in
the charges in the xLeap spreatsheet.

Does this sound reasonable? It's what I've been able to plan from
reading various tutorials and combining them. A question I have is do
you have to specify the coordination bonds to the nickel in xLeap/Amber
(You do in Spartan)? If you do, what type of nitrogens do I use for
the nitrogen atoms that coordinate to the nickel? Do I have to create
custom atom types? Do I have to specify bond angles, lengths, etc?

Or do I just create the ligand as a stand-alone structure, put the
nickel into its place and then have the program know that there is an
interaction due to the distance?

The compound is coordinated with nickel in a square-planar conformation
and the conformation is effected by its solvent environment appears to
effect the biological activity. I'm trying to model some theories as
to why this happens. I've spend time modeling the complex in Spartan
and would like to model the interaction of some of the results from
that program with a DNA 10mer. I can export from that program into a
variety of file types (pdb, mol2, etc) but have generally used pdb
files to prep things for Amber.


Kara Di Giorgio

On Feb 21, 2005, at 5:33 PM, David A. Case wrote:

> On Mon, Feb 21, 2005, Kara Di Giorgio wrote:
>> I'm trying to format a smallish organometallic compound. It contains a
>> crown-ether-like organic portion surrounding a Nickel atom. It has
>> nitrogen atoms in the crown coordinating with the Nickel.
> It's not clear whether you have looked at the crown ether tutorial:
> Even though you have a different ligand and a different metal ion, the
> principles should be the same. You will mostly have to do things on
> your own
> here: antechamber might help for the ligand, but it won't know anything
> about the metal ion.
> ...dac
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Received on Tue Feb 22 2005 - 22:53:00 PST
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