[gmx-users] drug-enzyme simulation.

[Tsjerk Wassenaar]

Hi Neha,

I guess you're referring to John Kerrigans tutorial, but it would
usually help if you specified the one you're using. I think the
tutorial should have a sentence stating that the ligand mayb be seen
away from the protein during the simulations, but that that is due to
the periodic boundary conditions. On another note, protein-ligand
interactions is one step further than 'performing simulations' and I
think you'd be better of first taking a tutorial on plain protein
simulations. The one I linked on the gromacs wiki
(http://nmr.chem.uu.nl/~tsjerk/course/molmod/) specifically addresses
issues such as PBC jumps, and some other basic stuff, which may help
you to get a feel for the things you may encounter when doing
simulations.

Cheers,

Tsjerk

On Sun, Mar 29, 2009 at 3:30 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> Many thanks Justin,
>
> It worked!
>
> 2009/3/29 Justin A. Lemkul <jalemkul at vt.edu>:
>>
>>
>> Neha Gandhi wrote:
>>>
>>> Hi List,
>>>
>>> 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated
>>> annealing followed by  production runs of 5ns usng NPT and PBC and
>>> PME.. After 5ns, the protein moves far away from the ligand.  I
>>> checked the 4ns gro files, the ligand and protein are bound together,
>>> but its only that 5ns gives issues.
>>>
>>> 2) I ran another similar but smaller system and the complex is stable
>>> even after 8ns.
>>>
>>> What went wrong with the simulations in case 1? Is there a way to fix
>>> this problem?
>>
>> Did the protein and/or ligand cross a periodic boundary?  If so, trjconv can
>> "fix" this visualization artifact.
>>
>> -Justin
>>
>>> Your help is much appreciated.
>>>
>>>
>>> Regards,
>>> Neha Gandhi,
>>> School of Biomedical Sciences,
>>> Curtin University of Technology,
>>> GPO Box U1987 Perth,
>>> Western Australia 6845
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623