Hi there,
I am trying to run MD on a porphyrin molecule which is custom made. The
porphyrin has a zinc center so antechamber doesn't handle it well. To work
around this, I made a residue including the porphyrin without zinc and used
antechamber to assign all the bonds, then I made an isolated zinc molecule
(with coordinates at the center of the porphyrin) and manually assigned a
charge in xleap. I then combined these in a pdb file as two different
residues and manually added in bonds to the zinc atom.
The minimization of the molecule seemed to work, but during the molecular
dynamics nothing is happening and I am not sure why. I am a new AMBER user
so I am not 100% sure I correctly assigned everything. Are there any issues
in my approach? Any help would be much appreciated.
Here is what I have in my input file for MD:
MD for porphyrin unit
&cntrl
imin = 0,
irest = 0,
cut = 12.0,
nstlim = 10000, dt = 0.001,
ntpr = 1, ntwx = 1, ntwr = 1
/
Thank you,
Amber
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Received on Fri Sep 18 2015 - 10:00:05 PDT
