[Chimera-users] ViewDock Data Analysis

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 23 10:32:30 PDT 2013


Hi Andrés,
The scores: energy, RMSD lb (lower bound) and RMSD ub (upper bound) of a docked ligand are calculated by AutoDock Vina and are described in the manual for that program:

<http://vina.scripps.edu/manual.html#output>

Basically they say energy is in kcal/mol (only a prediction, of course) and the RMSD values just indicate how similar each position is to the best-scoring position that was found in that run.  I'll add the link above to the manual page in Chimera so that others can find it more easily.

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Jul 23, 2013, at 8:29 AM, felipe vasquez <anfelvas at gmail.com> wrote:

> I have been executing a couple of docking processes through Autodock vina module in Chimera. Nevertheless, I am a bit confused about the docking analysis, because although I obtained a score for a certain number of ligand poses, I do not know if this number (-9.2, as an example) is expressed in kcal/mol, kj/mol, or even another units. On the other hand, I could not understand the meaning of RMSD l.b and RMSD u.b. What are they? and what role the play in the docking analysis procedure? 
> 




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