AMBER Archive (2008)

Subject: Re: AMBER: Calculate the RESP charge Fe3+ of heme (p450)

From: David A. Case (case_at_scripps.edu)
Date: Fri May 23 2008 - 00:35:29 CDT

On Fri, May 23, 2008, chen bents wrote:
>
> I want to get the RESP charge of heme(p450) , i got that ESP
> charge use gaussia03 software.and then use the antechamber programme of
> AMBER ,because i want to get the gaff of heme.When i run the command :
> antechamber -i cys.mol2 -fi mol2 -o cys.ac -fo ac -c rc -cf qout_stage2
> .There was a erro: For atom[1]:Fe1, the best APS is not zero, exit

GAFF is not set up to handle porphyrins. You might want to look at the heme
parameters in the contrib subdirectory, then modify them by hand for your
charges, and make whatever other changes are made (e.g.adding and Fe-S bond).
You'll have to do some work by hand.

Also, doing a literature search on P450 parameters will probably help as well:
there have been lots of force field simulations of these systems.

...dac

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