Ana Carolina Corrêa de Sousa

What is the impact of the reproducibility of a VS regarding to the random seed?

Can I change the random seed as I'm trying to reproduce some results using vina on pyrx? I mean, reproducing a vs, with the same parameters including the same random seed used on the first time. Thanks

Dear Sarkis, So, multiple rounds of energy minimization using Zinc database worked. Thank you very much. Best Regards, Ana

Dear Sarkis, That is what I've been doing. Still not working. Please help me out here. regards

I've increased the number of steps from 200 to 400 and changed the algorithim to Steepest Descent. Everything worked fine. But please notice that the problem is when I convert the compounds to PDBQT. The error has beeen generated on this step. Also notice that it is making the molecule completely flat As I described before, this is happening when I convert all the molecules to pdbqt. When I do one by one, this is not happening. But I cannot go one by one in a large set of compounds. Seems like a...

I've increased the number of steps from 200 to 400 and changed the algorithim to Steepest Descent. Everything worked fine. But please notice that the problem is when I convert the compounds to PDBQT. The error has beeen generated on this step. Also notice that it is making the molecule completely flat As I described before, this is happening when I convert all the molecules to pdbqt. When I do one by one, this is not happening. Seems like a bug to me. Please check the prints attached. Kind regards,...

I've increased the number of steps from 200 to 400 and changed the algorithim to Steepest Descent. Everything worked fine. But please notice that the problem is when I convert the compounds to PDBQT. The error has beeen generated on this step. Also notice that it is making the molecule completely flat Please check the prints attached. Kind regards, Ana