[gmx-users] trouble minimizing structure with mdrun

[Jack Shultz]

maybe I should go directly from pdb2gmx to grompp seeing as I have
already solvated and ionized the protein in VMD.

On Mon, Jan 4, 2010 at 8:04 PM, Jack Shultz <js at drugdiscoveryathome.com> wrote:
> 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
>



-- 
Jack

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