Hi Alberto,<br>
<br>
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.<br>
<br>
Good luck!<br>
<br>
Tsjerk<br>
<br><br><div><span class="gmail_quote">On 9/26/05, <b class="gmail_sendername">Alberto Malvezzi</b> <<a href="mailto:malvezzi@iq.usp.br">malvezzi@iq.usp.br</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear friends,<br>I am trying to make my simulation reproduce the same conformation found<br>in a crystal ligand-protein complex structure (for validation purpose).<br>Does anyone have experience with this?<br>At what temperature should I run my simulation?
<br>Should there be any special constraints?<br>Thanks for the help.<br>Alberto<br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>