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?
participants (2)
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Elaine Meng
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felipe vasquez