AMBER Archive (2005)

Subject: AMBER: Formatting Questions

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Mon Feb 21 2005 - 13:09:44 CST

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.

1. What would be the best way to assign atom types? Is it possible to
use antechamber to assign most of the atom types? Can the gaff force
field be used with a nickel-containing compound?

2. Is there somewhere that lists the possible atom types? Is there an
atom type already defined for a nitrogen coordinated to a metal? (One
is a pyridine nitrogen, the other three are either amine or imine
nitrogens, depending)

3. I have the molecule optimized in Spartan using Density Functionals.
  I was going to use charges from there and enter them in xLeap like was
done in the Non-Standard Residues tutorial. Does this sound
reasonable?

Thanks for any help,

Kara Di Giorgio

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