[AMBER] Relaxing a heme molecule

From: Amber Maharaj <amber.maharaj.uoit.net>
Date: Mon, 13 Jul 2015 16:02:17 -0400

Hi everyone,

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

antechamber -fi pdb -i heme.pdb -fo mol2 -o heme.mol2
parmchk -i heme.mol2 -f mol2 -o heme.frcmod

(load tleap and parameters again)
loadamberparams heme.frcmod
heme = loadmol2 heme.mol2
saveamberparm heme heme.prmtop heme.inpcrd

For the minimization input file, I used these options:
  ntb = 0,
  ioutfm = 1,

Thank you,
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Received on Mon Jul 13 2015 - 13:30:02 PDT
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