Autodock Vina Global Settings is not saved during docking

[lsegura1]

Hello. First off, this is a great program. I have developed automated scripts for similar processes but the GUI is very nice and clean, not to mention fast at molecular docking.

Only one problem I had: After trying to change the global settings of the autodock vina to output 20 poses, increase exhaustiveness, increase energy range, increase CPU, and increase binding modes, the settings did not remain and were not used when performing molecular docking. I tried saving those settings for each receptor and even saving grid box after saving the settings to see if it would do anything. Is there a reason the global settings are not being saved for the molecular docking?

Is there anything I can do on my end for this to work?

Thank you in advance and have a wonderful week!

[lsegura1]

One additional thing! It looks like the output poses of the protein-ligands has combined the atoms of all of the ligands in the multi-ligand sdf file into one so not the docked ligand poses are distorted and it is not outputting molecular docking data for each ligand in the sdf file.

[lsegura1]

Update! Just tried it again and this is what worked:

• My ligands were fixed and docked as separate compounds when I split the multi-ligand sdf files into multiple sdf files and imported the ligands just as multiple separate sdf. And then, instead of using autodock tools to prepare the ligands, I used open babel in the GUI (I will try this out with autodock tools again because I have a feeling that the problem with the ligand atoms being joined in as "one ligand" when docking had to do with the program having to look at a multi-ligand sdf file instead of split sdf ligand files)

• When trying to change the global settings for Vina, it seemingly does not save when you try and open the global settings to double check the numbers are saved, but when you run the docking, it does output the 20 poses instead of the default 9 for each ligand so this indicates that the global settings were saved, they just do not show that they are when you open up global settings again to double check.

Please let me know, if you think there is anything else I should know or try out. This is very exciting seeing that all of the work I have to do with multiple python and shell scripts can now be done in one place with ease and swiftness. Amazing work :)

Best,