Thanks Mark and Justin.<br> <br> I did experiment with the following editconf. It works. Thanks. <br> <br> editconf -f ${file}.gro -o ${file}_box.gro -d 0.75 -bt cubic<br><br> By the way, how to select box size automatically ? I just gave an arbitrary number: 0.75<br>
<br> Another question is how to get the structure with lowest energy from *.trr ?<br><br> When I used the following command: <br> trjconv -f ${file}.minim_traj.trr -s ${file}.input.tpr -o ${file}.minim_traj.pdb <br>
<br> It outputs 15 MODELS with t= 125.00000 t= 252.00000, t= 379.00000 , ...t= 2001.00000<br><br> I guess t= 2001.00000 has the lowest energy.<br><br> Best<br><br><br><br><div class="gmail_quote">On Tue, Mar 11, 2008 at 5:58 PM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">> Hi,<br>
><br>
> I used a script given below for energy minimization of a native<br>
> protein-protein complex 1akj.<br>
><br>
> I removed HETATMs and water molecules from the structure, and the<br>
> minimized<br>
> structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80.<br>
> Then I used rasmol to check the result. The ligand is ran away from<br>
> receptor.<br>
> rasmol 1akj_oplsaa.minim_traj.pdb<br>
<br>
</div>As Justin said, you might well be observing a PBC artefact. Having not<br>
turned off PBC in your .mdp file, or used editconf to change the size of<br>
the box that pdb2gmx chooses, then your EM is probably using defaults that<br>
you'd rather not use.<br>
<div class="Ih2E3d"><br>
> Then I tried the larger epsilon_r = 800000.0, and got very<br>
> similar result. I mean that for two substantially different values of the<br>
> epsilon_r minimization gives absolutely the same final positions of the<br>
> ligand.<br>
<br>
</div>Being good scientists, we deduce that the approximate location of the<br>
local energy minimum from this starting point is not dependent on the<br>
dielectic of the medium. :-)<br>
<div class="Ih2E3d"><br>
> I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1,<br>
> G45a3, G53a5, G53a6, gmx, oplsaa.<br>
> I also got similar result.<br>
<br>
</div>Likewise.<br>
<font color="#888888"><br>
Mark<br>
</font><div><div></div><div class="Wj3C7c"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Research Assistant<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone: (785) 864-1962