<div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif">Hi Elaine,</div><div class="gmail_default" style="font-family:verdana,sans-serif"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif">
Thanks a lot for your help and the link you added.</div><div class="gmail_default" style="font-family:verdana,sans-serif"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif">Regards,</div></div><div class="gmail_extra">
<br clear="all"><div><div dir="ltr"><div><div><font face="verdana, sans-serif"><b>Andrés Felipe Vásquez J., MSc.</b><br>Grupo de Fisiología Molecular</font></div><div><font face="verdana, sans-serif">Subdirección de Investigación Científica y Tecnológica</font></div>
<div><font face="verdana, sans-serif">Dirección de Investigación en Salud Pública<br>Instituto Nacional de Salud<br>Avenida calle 26 No. 51-20 - Zona 6 CAN<br>Bogotá, D.C., Colombia<span style="font-size:small"> </span></font><br>
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<br><br><div class="gmail_quote">2013/7/23 Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Andrés,<br>
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:<br>
<br>
<<a href="http://vina.scripps.edu/manual.html#output" target="_blank">http://vina.scripps.edu/manual.html#output</a>><br>
<br>
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.<br>
<br>
I hope this helps,<br>
Elaine<br>
----------<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
On Jul 23, 2013, at 8:29 AM, felipe vasquez <<a href="mailto:anfelvas@gmail.com">anfelvas@gmail.com</a>> wrote:<br>
<br>
> 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?<br>
><br>
<br>
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