Hello, 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.
regards, wk yeo ________________________________ Date: Tue, 7 Oct 2008 11:36:57 +0530 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED]; gmx-users@gromacs.org Subject: Re: [gmx-users] setting constraints to incomplete protein structures CC: Hi yeo, I have one query related to the MD you are trying. 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) I am also trying the same, But not finding any criteria to pick up the conformation of protein to try it further for docking ? Do you have any insight into the same ? With Thanks, Vivek _________________________________________________________________ Easily publish your photos to your Spaces with Photo Gallery. http://get.live.com/photogallery/overview _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
