VMD-L Mailing List
From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Sep 24 2013 - 10:35:31 CDT
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Actually, it can happen if there's more than one hbond between the residue and the ligand some of the time (if I recall correctly, they get double counted). You could check your multimer idea by selecting only one subunit to run the hbonds calculation on.
One way to get an accurate count, I suppose, would be to export a time series for that residue and ligand and count the frames where it's zero.
On Sep 24, 2013, at 11:03 AM, Stephan Schott wrote:
> Hi to all VMD users,
> I've been using VMD to analyze the hbonds from a Desmond trajectory file I have of a protein of my interest and a ligand. The problem comes from the results; the details say that there is more than 100% of occupancy of one of the protein residues with the ligand. I think that this happens because the protein is a multimer, so the plugin adds the occupancy of the same residues from different subunits as it was just one, but I want a confirmation of this suspicion. Has anyone seen this kind of results? Waiting for any suggestion,
>
> --
> Stephan Schott V.
> Licenciado en Bioquímica
> Tesista en Laboratorio de Enzimología Molecular
> Universidad Austral de Chile
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