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:
> http://www.pharmacy.manchester.ac.uk/bryce/amber/ and have used the
> following commands to generate a heme molecule.
>
> tleap -s -f leaprc.gaff
> loadamberparams hemall.pcy
> loadamberprep heme_all.in
> 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 Mon Jul 13 2015 - 18:00:02 PDT
