Re: [AMBER] issues

From: David A Case <>
Date: Wed, 20 May 2015 07:48:18 -0400

On Tue, May 19, 2015, David Poole wrote:
> I've been attempting to use the tool-chain to build amber
> parameters for a iron porphyrin IX, heme, system, and have been having a
> few difficulties that may be related.

I'll let Pengfei or others deal with issues, but it is not clear to me
that this is the best tool for building a complex ligand environment like a
porphyrin. Your main challenge here involves the large organic ligand. You
might consider starting with force fields that are already available, such
as that from

or as described in Shahrokh, K; Orendt, A; Yost, G. and Cheatham
III, T. E. "Quantum mechanically derived AMBER-compatible heme
parameters for various states on the cytochrome P450 catalytic cycle"
J. Comp. Chem. (2011)

You could modify these for any deficiencies you see from your quantum
modeling. (For example, you might wish to get a new charge model, and tailor
the force constants involving iron to suit the exact environment you have.


[Cheatham group: can we(you) upload the Shahrokh files to the Manchester

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Received on Wed May 20 2015 - 05:00:03 PDT
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