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
quit
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:
&cntrl
imin=1,
ntx=1,
irest=0,
maxcyc=2000,
ntmin=1,
ncyc=1000,
ntb = 0,
ntpr=1,
ntwx=1,
ioutfm = 1,
cut=10.0,
/
Thank you,
Amber
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Received on Mon Jul 13 2015 - 13:30:02 PDT
