AMBER Archive (2008)

Subject: Re: AMBER: Problem running implicit minimization

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Tue Mar 04 2008 - 00:17:27 CST

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_at_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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