Hi, 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? Best regards, *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
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@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?
Hi Elaine, Thanks a lot for your help and the link you added. Regards, *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@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@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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Elaine Meng -
felipe vasquez