Re: [AMBER] Relaxing a heme molecule

From: Amber Maharaj <>
Date: Wed, 15 Jul 2015 15:26:49 -0400

Thank you for the reply.

I have another question, as I was only temporarily working with the heme
molecule. Ultimately what I want to do is create a zinc centered porphyrin
with octyloxy side chains. Once I get this structure, I need to link
several porphyrins into a nanoring of 10 or 12 porphyrin units.

I didn't directly tackle this at first since I was having some trouble
working with the zinc center of the porphyrin. This is why I was trying to
work with a similar molecule like heme to gain some insights about the
process. Would I need to generate my own parameters to get a viable
structure? Any suggestions on how to proceed?

Thanks again in advance,

On Mon, Jul 13, 2015 at 8:35 PM, case <> wrote:

> On Mon, Jul 13, 2015, Amber Maharaj wrote:
> >
> > I am new to AMBER and have run into a problem with relaxing a heme
> > molecule. My starting geometry appears to be reasonable, however when I
> > relax it, the iron atom jumps out of plane. It is my understanding that
> > transition metals may require special attention in AMBER, however I do
> not
> > know what triggered this result and what I can change to fix it. Any help
> > would be greatly appreciated.
> >
> > I'm using the heme (all-atom) frcmod and prep files from this site:
> > and have used the
> > following commands to generate a heme molecule.
> >
> > tleap -s -f leaprc.gaff
> > loadamberparams hemall.pcy
> > loadamberprep
> > savepdb HEM heme.pdb
> > quit
> This heme was meant to be part of a myoglobin-like protein: hence it needs
> to be bonded to a histidine or similar ligand, and to a sixth ligand like
> O2 or CO. Only under these circumstances will the iron stay in the plane
> of
> the porphyrin.
> As you note, species with transition metals generally only give good
> results
> in limited environments, and it is often problematic to use them outside of
> their intended ones.
> ....dac
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Received on Wed Jul 15 2015 - 12:30:02 PDT
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