AMBER Archive (2008)

Subject: Re: AMBER: reg-antichamber run

From: FyD (
Date: Thu Dec 11 2008 - 03:57:26 CST

Quoting balaji nagarajan <>:

> On Wed, Dec 10, 2008, balaji nagarajan wrote:
>> I tried in building the parameter and topology for
>> cobalt(III) hexammine (3+) using antichamber .
> Antechamber deals with organic molecules: it doesn't know how to deal with
> metal ions.

You might also decide to use R.E.D. which is fully compatible with
metals (with chemical elements up to Br in the periodic table).

The key points are to build a correct P2N file. See the corresponding
& to check that the atom connectivities are correct in the initial P2N
file; (as those connectivities are used to generate the correct
molecular topology in the force field library generated - Tripos mol2
file format).

regards, Francois

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