Thanks again for providing Smina! I just started learning docking and I am not very clear about the default procedure without --minimize argument. Learned from orgininal AutoDock Vina, docking consists of several independent runs and each contains steps performing pose perturbation, local minimization and decision on accepting/rejecting the new pose. Do the program only samples and scores poses by default (without --minimize)?
Thanks in advance!
Add on:
I seems to be a misunderstanding from my part. I tested with --minimize and it only performed local minimization (much faster than actual docking). Now I consider it is an alias for --local_only (https://sourceforge.net/p/smina/discussion/help/thread/27839abf/#3399).
Based on this, I am assuming the default steps for docking (including local minimization) is performed without --minimize?
Last edit: Yuning Shen 2020-09-27
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Thanks for clarifiation - I did see slight difference in results between using --minimize and using --local_only for conformation optimization.
As convergence is one of the improvement of Smina over AutoDock Vina, does the default docking configuration (without --minimize or --local_only) also perform each local optimization to convergence?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi David,
Thanks again for providing Smina! I just started learning docking and I am not very clear about the default procedure without
--minimizeargument. Learned from orgininal AutoDock Vina, docking consists of several independent runs and each contains steps performing pose perturbation, local minimization and decision on accepting/rejecting the new pose. Do the program only samples and scores poses by default (without--minimize)?Thanks in advance!
Add on:
I seems to be a misunderstanding from my part. I tested with
--minimizeand it only performed local minimization (much faster than actual docking). Now I consider it is an alias for--local_only(https://sourceforge.net/p/smina/discussion/help/thread/27839abf/#3399).Based on this, I am assuming the default steps for docking (including local minimization) is performed without
--minimize?Last edit: Yuning Shen 2020-09-27
Correct. --minimize isn't quite the same as --local_only with vina as, unlike local_only, it actually will go to convergence.
Thanks for clarifiation - I did see slight difference in results between using
--minimizeand using--local_onlyfor conformation optimization.As convergence is one of the improvement of Smina over AutoDock Vina, does the default docking configuration (without
--minimizeor--local_only) also perform each local optimization to convergence?No, it keeps the quick local optimization of Vina when docking to keep things fast.