In Autodock4.2, we can set the number of GA runs for docking. However, in Autodock Vina, there is no option for specifying the number of runs. I was just wondering, how many runs actually Vina do for docking? My configuration file is as follows:
receptor = mag1_rigid.pdbqt
flex = mag1_flex.pdbqt
ligand = m6.pdbqt
out = out.pdbqt
center_x = 59.973
center_y = 87.806
center_z = 89.957
size_x = 56
size_y = 86
size_z = 64
Dear Manas!
Some of the lines in your configuration file is missing. Kindly find the complete config test file from the attachment.
We can able to adjust the GA runs
"num_modes = 10" (Representing 10 conformations)
Hi D. Mani Maran,
Thank you! I didn't write the num_modes because I used default condition where 9 conformations were generated. I know that the num_modes command represents the number of conformation that Vina will produce. But I was wondering, is it also representing the number of GA runs?
Upto my knowledge, I cant figure out from your query. But please go to the website as;
AutoDock Vina actually uses a united-atom scoring function.Unlike in AutoDock 4, in AutoDock Vina, each run can produce several results: promising intermediate results are remembered. These are merged, refined, clustered and sorted automatically to produce the final result.
Refer http://vina.scripps.edu/manual.html
Hi Sridhar Sundaram,
Thank you for your explanation. I think I understand it now. I already read the information on the website before. But since I'm new in this field, I don't have background so I don't really understand the mechanism beneath it.
Another thing is, what is the exhaustiveness really mean? What are the things that determine how much value of exhaustiveness that I should set? And is there any limit of exhaustiveness?
Hi Mr Manas
In my perspective exhaustiveness parameter determine number of search to find best conformation,actually you increase search detail so your docking time its be longer.
akbari
Hi Mr Akbari,
Okay. I understand now. Thank you very much! :)
Hi !
even if i am keeping exhaustiveness =15 or more , it's still giving me 9 conformations only ! Is there any way to increase the numbber of conformations ?
Manimaran D Sir ,what should be the specified number of runs in Autodock 4.2 ?
Are 50 runs enough ?
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