look at the minimization output and identify the atom with the GMAX at step
1.
then use a visualization program to see what is going on with that atom in
your
initial coordinates.
the total charge is not likely the problem.
On Tue, Mar 4, 2008 at 1:17 AM, Lili Peng <lpeng.ucsd.edu> wrote:
> Hi Dr. Case,
>
> Thanks for your advice. Now that I think about it, I'm guessing the
> minimization didn't really work because of the way I prepared my .crd and
> .top files in xLeap. My molecule is really negatively charged (charge of
> around -200), and xleap even warned me when I generated the crd and top
> files. I'm doing an implicit minimization here so I didn't add any ions or
> water molecules. But do you think I should add ions for the sake of
> neutralizing the system? I'm trying to pinpoint whether the highly negative
> charge of my molecule is disturbing the energetics of my system when I try
> to run the implicit minimization.
>
> Thanks,
> Lili
>
>
> On 03/03/2008, David A. Case <case.scripps.edu> wrote:
> >
> > On Mon, Mar 03, 2008, Lili Peng wrote:
> > >
> > > forrtl: severe (64): input conversion error, unit 9, file
> > > /nas/lpeng/nexil/nexil8/nexil8_even_min.rst
> >
> >
> > You have '****' entries in your restart file, indicating that something
> > bad
> > happened during the minimization. I don't think we have enough
> > information
> > to help more, but please look at the course of your minimization. You
> > may
> > have to carry it out in pieces, and use VMD or Chimera or some such tool
> > to
> > visualize the structures in order to help pin down the error.
> >
> > ....dac
> >
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>
>
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Received on Wed Mar 05 2008 - 06:07:31 PST
