Hi Yeo, Actually, I tried the same thing to get various conformation for the protein I am dealing with. For sampling the frames (i.e. conformation ) I tried two approaches... first I have taken frames which are at equal distance on trajectory without looking for any parameter ( randomly). Second approach I tried is on the basis of RMSD value.
But none of the approach worked for me, means I didn't got good results for docking. Do you have some better way or thought for it ? With Thanks, Vivek 2008/10/8 wk yeo <[EMAIL PROTECTED]> > > 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 >
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