Re: AMBER: prepin for metal centre

From: David A. Case <>
Date: Mon, 25 Jun 2007 17:43:26 -0700

On Mon, Jun 25, 2007, Mattias Blomberg wrote:
> I want to create a prepin file for a metal centre, which consists of a Mn,
> two Imidazole rings (modeling HIS), one acetate ion (modeling GLU) and an
> organic substrate. I've done an ESP calculation using Gaussian (IOp(6/33=2,
> 6/41=10, 6/42=8) scrf=(IEFPCM,read)). Then I ran Antechamber to produce a
> prepin file with the following command line
> antechamber -fi gout -fo prepi -i filename.out -o filename.prepi -c resp
> -at gaff -rn MNC

Antechamber cannot (currently) handle metal ions. The simplest procedure
is to use antechamber on each of the ligands (separately, and without the
metal), then use LEaP to put everything together. An example of how this can
be done for a copper complex that is similar to your Mn center is given here:

[Ross: I think we should move this onto the current tutorial page, because it
covers things that are not on the current list.]

...good luck...dac

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Received on Wed Jun 27 2007 - 06:07:26 PDT
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