AMBER Archive (2009)

Subject: Re: [AMBER] iron in prepi file generation for heme

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Dec 24 2009 - 11:27:07 CST

On Wed, Dec 23, 2009, Donald Keidel wrote:
>
> I have generated resp charges using gaussian and antechamber. I
> am trying to generate a prepi file that will include the Fe atom
> information for heme.
>
> I am getting the following error message when I execute the following command:
>
> command I execute: antechamber -fi mol2 -fo mol2 -i
> HEM_edited_H_pmv_marvin_babel.mol2 -o
> HEM_edited_H_pmv_marvin_babel_resp.mol2 -c rc -cf input.crg -j 4 -at amber

This will create a mol2 file "-fo mol2", not a prepi file. That is actually a
good thing...

>
> error: For atom[1]:Fe, the best APS is not zero, bonds involved by this
> atom are frozen

Gaff doesn't know about transition metals, and is not going to know what to
do with an iron atom in the center of a heme molecule.

>
> I then look at a prepi file I create from this...

It's not clear how you got the prepi file, given what you wrote above.

I'd suggest rather starting from the heme files in the contributed data base,
and hand-editing those to use the resp charges you have, and to change any
other parameters you don't like. Antechamber is just going to get confused
with an iron heme molecule.

....dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber