Re: [AMBER] How to deal with Heme?

From: David A Case <>
Date: Fri, 13 May 2016 08:21:04 -0400

On Thu, May 12, 2016, Morteza Chehel Amirani wrote:
> I'm wondering if anyone could help me to construct the mol2 and frcmod
> files. It seems gaff recognizes the iron as "f" which is not correct.

Antechamber does not deal with metal ions, but it does not give very
informative error messages when the input contains elements it is not equipped
to deal with. [Developers: this would be a great thing to fix, perhaps for
someone who wants to gain experience with the code.]

If you just have new charges, you can manually edit the existing HEM prep
files to use the charges you prefer. This is in some ways not ideal, but
working out an entire new parameterization for heme groups will be a big task.


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Received on Fri May 13 2016 - 05:30:05 PDT
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