[gmx-users] trouble minimizing structure with mdrun

[Jack Shultz]

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

http://boinc.drugdiscoveryathome.com/1YQW.zip

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
> --
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org