<div dir="ltr">Hi Yeo,<br><br>Actually, I tried the same thing to get various conformation for the protein I am dealing with. For sampling the frames (i.e. conformation )<br>I tried two approaches...<br>first I have taken frames which are at equal distance on trajectory without looking for any parameter ( randomly).<br>
Second approach I tried is on the basis of RMSD value.<br><br>But none of the approach worked for me, means I didn't got good results for docking.<br>Do you have some better way or thought for it ?<br><br>With Thanks,<br>
Vivek<br><div class="gmail_quote">2008/10/8 wk yeo <span dir="ltr"><<a href="mailto:vivacity@hotmail.com">vivacity@hotmail.com</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;">
<br>
Hello,<br>
<br>
Usually, the protein-ligand complexes which we download from the PDB contain ligands which I am not interested in. But I have other ligands which I think might be able to dock into the same binding pocket. Of course, it is a 'simple' matter of docking these 'new' ligands into the holo protein structure (obtained by deleting the original ligand). But I would like to think that most of the proteins obtained this way are only in conformations which are favourable for the original ligands. Therefore, I am guessing that conducting some short MD runs will allow the binding pocket to 'adapt' properly to the newly docked ligands and/or vice versa. At the moment, I have not been able to conduct the MD runs due to the problems discussed in my previous postings. But I foresee that I will have a dilemma over which conformation from the entire MD to use. Do I take the average (mean) conformation? Or do I take the last (final) conformation? The solutions will have to be found in the future once I get my MD running.<br>
<br>
regards,<br>
wk yeo<br>
<br>
________________________________<br>
<br>
Date: Tue, 7 Oct 2008 11:36:57 +0530<br>
From: <a href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a><br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>; <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: Re: [gmx-users] setting constraints to incomplete protein structures<br>
CC:<br>
<div class="Ih2E3d"><br>
<br>
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>
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