Hi Carlos,
I tried doing that by loading the .top and then .rst file in VMD, but
nothing showed up VMD. Maybe I'm doing something wrong in VMD..
Lili
On 04/03/2008, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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.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.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.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
> > > > >
> > > > >
> > > > > -----------------------------------------------------------------------
> > > > > The AMBER Mail Reflector
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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.gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
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Received on Wed Mar 05 2008 - 06:07:39 PST
