On Fri, Sep 18, 2015, Amber Maharaj wrote:
>
> 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.
We need to know more about what you mean by the phrase "nothing is happening".
(There is no program output? There is some output in the mdout file, but no
evidence of a real trajectory? The coordinates are not changing from their
initial values? something else?)
Try to see what might be different between your files and those in a simple
test case like the one in $AMBERHOME/test/dhfr/Run.dhfr.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 18 2015 - 12:00:04 PDT
