AMBER Archive (2008)

Subject: Re: AMBER: Problem running implicit minimization

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Tue Mar 04 2008 - 17:25:32 CST

Yeah, I looked in the GMAX of the output file and the energy was increasing,
not dropping. So I tried increasing the maxcyc to 5000 and the ntpr=100,
but looking at the output file, the system was barely making it past cycle
number 300. What if I change the ncyc? it's currently at 250.

I'm concerned about the steric clashes throwing the energetics of my system
off-course. What if I try to minimize my system in vacuum beforehand?

Thanks,
Lili

On 04/03/2008, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> 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_at_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_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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> >
> >
>
>

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