[gmx-users] setting constraints to incomplete protein structures

vivek sharma viveksharma.iitb at gmail.com
Wed Oct 8 06:39:05 CEST 2008

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
Do you have some better way or thought for it ?

With Thanks,
2008/10/8 wk yeo <vivacity at hotmail.com>

> 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: viveksharma.iitb at gmail.com
> To: jalemkul at vt.edu; gmx-users at 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
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