[gmx-users] trouble minimizing structure with mdrun

Jack Shultz js at drugdiscoveryathome.com
Tue Jan 5 02:04:03 CET 2010

I did a little more checking on the structures, I notice the results
from genion move part of the protein far outside the solvent box. I
shall try this without the genion step
I put all the files in the working directory for this preperation in a
zip archive under


On Mon, Jan 4, 2010 at 2:22 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Jack,
>> On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>> Hi Jack,
> <snip>
>>> After preparation with (V|NA)MD, did pdb2gmx correctly assign chains,
>>> or did it tie chains together? In the latter case it would have issued
>>> a number of "Long Bond Warnings". Did anything else odd show up in
>>> the output of any of those steps? Did you actually read through it?
> Post pdb2gmx/grompp output to help us help you.
> Cheers,
> Tsjerk
> --
> Tsjerk A. Wassenaar, Ph.D.
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php



More information about the gromacs.org_gmx-users mailing list