| Index | Recent Threads | Unanswered Threads | Who's Active | Guidelines | Search |
 |
World Community Grid Forums
Category: Active Research
Forum: Smash Childhood Cancer
Thread: Autodock Vina and....Smina |
| No member browsing this thread |
|
Thread Status: Active Total posts in this thread: 15
|
|
| Author |
|
|
[VENETO] boboviz
Senior Cruncher Joined: Aug 17, 2008 Post Count: 183 Status: Offline Project Badges: 
|
From details page:
The molecular structure of each ligand and target molecule, showing where all of the atoms are positioned, are run through a research software tool called AutoDock VINA .Vina is a good tool, but the latest version was May 2011. Smina is a fork of Autodock Vina, costantly updated and with this features: Changes from the standard Vina (version 1.1.2) include: -comprehensive support for ligand molecular formats (via OpenBabel)* -support for multi-ligand files (e.g., an sdf file)* -support for addition term types (e.g., desolvation, electrostatics) -support for custom, user-parameterized scoring functions (see --custom_scoring) -automatic box creation based on a user-specified bound ligand -allow the output of more than 20 docking poses -vastly improved minimization algorithms (--minimize goes to convergence) -*experimental* easily define flexible residues of receptor (--flexres and --flexdist) For workflows where AutoDock Vina is used for minimization (local_only) as opposed to of docking, these changes make Vina much easer to use and 10-20x faster. Docking performance is about the same since partial charge calculation and file i/o isn't such a big part of the performance. Why not to try to use it?? |
||
|
|
Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3295 Status: Offline Project Badges: 
|
Well, I'm sure the scientists have their reasons.
----------------------------------------From what you post though, SCC wouldn't benefit from a performance boost. AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W AMD Ryzen 7 7730U 8C/16T 3.0 GHz [Edit 2 times, last edit by Falconet at Jan 27, 2017 9:22:46 PM] |
||
|
|
KLiK
Master Cruncher Croatia Joined: Nov 13, 2006 Post Count: 3108 Status: Offline Project Badges: 
|
Great, so SMINA can go on Androids! ;)
---------------------------------------- |
||
|
|
branjo
Master Cruncher Slovakia Joined: Jun 29, 2012 Post Count: 1892 Status: Offline Project Badges: 
|
?
---------------------------------------- Crunching@Home since January 13 2000. Shrubbing@Home since January 5 2006  |
||
|
|
[VENETO] boboviz
Senior Cruncher Joined: Aug 17, 2008 Post Count: 183 Status: Offline Project Badges:
|
Well, I'm sure the scientists have their reasons. Or, maybe, they don't know the existance of this tools From what you post though, SCC wouldn't benefit from a performance boost. Why not?? For workflows where AutoDock Vina is used for minimization (local_only) as opposed to of docking, these changes make Vina much easer to use and 10-20x faster. |
||
|
|
[VENETO] boboviz
Senior Cruncher Joined: Aug 17, 2008 Post Count: 183 Status: Offline Project Badges:
|
Great, so SMINA can go on Androids! ;) I don't know if it runs on android. I know they are working on a gpu version of vina/smina, named gnina, but is not ready for production... |
||
|
|
Jim1348
Veteran Cruncher USA Joined: Jul 13, 2009 Post Count: 1066 Status: Offline Project Badges: 
|
I know they are working on a gpu version of vina/smina, named gnina, but is not ready for production... How broadly applicable that is will of course have to be determined, but with all the Vina projects around here, it should be looked at carefully by someone. |
||
|
|
KLiK
Master Cruncher Croatia Joined: Nov 13, 2006 Post Count: 3108 Status: Offline Project Badges:
|
Great, so SMINA can go on Androids! ;) I don't know if it runs on android. I know they are working on a gpu version of vina/smina, named gnina, but is not ready for production... from what I can tell, it's going to be CUDA based...so nVIDIA card are OK!  |
||
|
|
Jim1348
Veteran Cruncher USA Joined: Jul 13, 2009 Post Count: 1066 Status: Offline Project Badges:
|
from what I can tell, it's going to be CUDA based...so nVIDIA card are OK! Even better; what more could we ask for? |
||
|
|
Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3295 Status: Offline Project Badges:
|
Well, I'm sure the scientists have their reasons. Or, maybe, they don't know the existance of this tools From what you post though, SCC wouldn't benefit from a performance boost. Why not?? For workflows where AutoDock Vina is used for minimization (local_only) as opposed to of docking, these changes make Vina much easer to use and 10-20x faster. Well.... "Docking performance is about the same since partial charge calculation and file i/o isn't such a big part of the performance." ... we are docking. That 10-20x boost is for "minimization", whatever that is. AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W AMD Ryzen 7 7730U 8C/16T 3.0 GHz [Edit 1 times, last edit by Falconet at Jan 28, 2017 7:10:42 PM] |
||
|
|
|