[gmx-users] crystal ligand-protein complex

[Tsjerk Wassenaar]

Hi Alberto,

What you want to do in such a case is to simulate the actual crystal. That
is probably the only environment in which that specific conformation occurs
(for reasonable amounts of time). To do so you need to have a periodic unit
cell created from the original space group, with the appropriate number of
copies of the protein-ligand complex. Than add water to fill up the gaps
between the units and run with pressure coupling (and of course energy
minimization, position restraint MD). You can take either room temperature
or the temperature at which the diffraction was determined, but this will
most likely only affect the fluctuations and not the conformation on the
usual time scales.

Good luck!

Tsjerk


On 9/26/05, Alberto Malvezzi <malvezzi at iq.usp.br> wrote:
>
> Dear friends,
> I am trying to make my simulation reproduce the same conformation found
> in a crystal ligand-protein complex structure (for validation purpose).
> Does anyone have experience with this?
> At what temperature should I run my simulation?
> Should there be any special constraints?
> Thanks for the help.
> Alberto
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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