[Chimera-users] ViewDock Data Analysis

felipe vasquez anfelvas at gmail.com
Wed Jul 24 09:08:48 PDT 2013

Hi Elaine,

Thanks a lot for your help and the link you added.


*Andrés Felipe Vásquez J., MSc.*
Grupo de Fisiología Molecular
Subdirección de Investigación Científica y Tecnológica
Dirección de Investigación en Salud Pública
Instituto Nacional de Salud
Avenida calle 26 No. 51-20 - Zona 6 CAN
Bogotá, D.C., Colombia

2013/7/23 Elaine Meng <meng at cgl.ucsf.edu>

> 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
> ----------
> 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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