AMBER Archive (2008)

Subject: Re: AMBER: reg-antichamber run

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Dec 11 2008 - 03:57:26 CST

Quoting balaji nagarajan <balaji_sethu_at_hotmail.com>:

> 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.
http://q4md-forcefieldtools.org/RED/ 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
tutorial:
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
& 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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