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Can't load ligands for AutoDock_Vina in PyRx 0.9.2

PostPosted: Fri Jul 08, 2016 8:37 am
by Jae
I bought PyRx version 0.9.2 for Windows and already update PyRx. But when I tried to load about 30,000 ligands the error message shown is "Common dialog failed with error code 3003". What should I do to solve this, please? Also, when I tried AutoDock_Vina with 3 ligands, I found that all saved SDF file from each row (in Analyze Result tab) are the same (one) structure of only one position (conformation). How could I get the structure of each docking ligand in correct position and in corresponded to each Vina row result, please? Regarding the computer spec, it is 64 bits Windows 8.1 running on core i7-4770 CPU with 28 GB DDR3 RAM, with NVIDIA GeForce 980Ti card, and about 100 GB free on both C drive (program installed in this drive) and data drive. Thank you so very much in advance.

Re: Can't load ligands for AutoDock_Vina in PyRx 0.9.2

PostPosted: Fri Jul 08, 2016 2:01 pm
by sargis
Thank you for purchasing PyRx. I haven't tried to load about 30,000 ligands, but I know that some users were able to work with that large amount of ligands. I haven't seen error code 3003 and googling it I came across a site that indicates it might be hardware/RAM decline error. I would try any repair tool from a questionable site though.

Your computer specs look good. I have an HP computer with 64 bits Windows 7 and 8 GB RAM. If you can send me the ligand file, I can try this on my computer to see if I can reproduce this error.

Regarding saved SDF file, there is a preferences option called "Number of Poses to Retain" accessible through Edit > Preferences > Open Babel > AutoDock Ligand. Please change the default from 1 to 0 to retain all the poses. There is a screenshot of this dialog at viewtopic.php?f=25&t=1384#p3335

I've changed this in the latest version, but preferences options stay the same when you update.