<div dir="ltr">Hi yeo,<br>I have one query related to the MD you are trying.<br> What I understood here is you are trying different conformation of your protein molecule for docking it with ligand (please, correct me if I am wrong)<br>
I am also trying the same, But not finding any criteria to pick up the conformation of protein to try it further for docking ?<br>Do you have any insight into the same ?<br><br>With Thanks,<br>Vivek<br><br><div class="gmail_quote">
2008/10/7 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><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"><br>
<br>
wk yeo wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
My responses are as follows:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
My questions:<br>
1) Is it a good idea to use such catalytic domain structures for MD simulation? Or should I only use complete protein structures for MD?<br>
</blockquote>
That depends entirely upon what you are interested in simulating.<br>
</blockquote>
<br>
I am interested in predicting the binding energy (via further processing using a docking software) of a ligand to a specific protein target based on the conformation of the binding pocket after MD. How will missing residues in the other parts of the protein target affect the MD run for such purposes?<br>
<br>
</blockquote>
<br></div>
In biology, structure leads to function. Missing residues may lead to spurious behavior, such as destabilization of the protein structure.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to constraint any atoms at the 'edges' during the MD run?<br>
</blockquote>
What kind of "edges?" Those that are adjacent to the missing segments? If<br>
that's what you mean, see distance *restraints* or position *restraints*.<br>
</blockquote>
<br>
Yes, I meant atoms that are adjacent to the missing segments. When should I use distance restraints and when should I use position restraints?<br>
<br>
</blockquote>
<br></div>
Distance restraints are what you are probably looking for. You can fix the distance between the backbone atoms to the distance found in the crystal structure. As for whether or not you can be confident in doing so is up to you.<br>
<br>
Position restraints are typically applied during solvent equilibration to allow the solvent to orient around the solute.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have a new question: What if the protein-ligand complex structure obtained from PDB contains chloride ions? How should I handle any ions during the MD runs? Restraint them as well? Or should I just let them go through MD without any restraints?<br>
<br>
</blockquote>
<br></div>
If the ions were part of the precipitant or some sort of stabilizing co-solvent, they may be unnatural and therefore safe to ignore. Adding (at least) counterions to an MD simulation is routine, so you may end up adding those ions back within during solvation.<br>
<font color="#888888">
<br>
-Justin</font><div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
regards,<br>
wk yeo<br>
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</blockquote>
<br></div><div class="Ih2E3d">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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