AMBER Archive (2008)

Subject: Re: AMBER: Problem running implicit minimization

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Mar 04 2008 - 17:39:23 CST

did you visually look at the area around the atom with gmax?
that might help to see what's causing the problem.

On Tue, Mar 4, 2008 at 6:25 PM, Lili Peng <lpeng_at_ucsd.edu> wrote:

> 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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> > >
> > >
> >
> >
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
===================================================================

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