Re: [AMBER] issues

From: Pengfei Li <>
Date: Wed, 20 May 2015 10:24:02 -0400

Hi David,

Sorry for the late reply. Here the main thing is the program consider the
Fe atom in HEM as a F atom. This bug dues to that I made all the element
inside a residue except ion residues use the first letter as its element.

The way to solve the problem is extract the Fe ion out from the HEM residue
as an independent residue with residue name "FE" and atom name "FE" if it
is Fe3+ or residue name "FE2" and atom name "FE2" if it is Fe2+. In this
way the software could recognize the Fe ion normally.

You may also try the existing parameters suggested by Dave. It would be a
quick way to build the model and also a good way to do a quick check about
whether the newly generated parameters by are correct.

Hope that helps,

2015-05-20 7:48 GMT-04:00 David A Case <>:

> 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.
> ....dac
> [Cheatham group: can we(you) upload the Shahrokh files to the Manchester
> server?]
> _______________________________________________
> AMBER mailing list

Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
AMBER mailing list
Received on Wed May 20 2015 - 07:30:03 PDT
Custom Search