Doubts on minimisation

User fa9047b33c

21-04-2015 22:36:45


What would be the best steps to do a minimisation procedure in Marvin 15.2.9 having in mind that I'm preparing ligands for docking? Is it better to use conformers or moldyn?

2nd part of the question: if using moldyn is there anyway to selecrt only the lowest energy conformation from the command line?


thank you for your help

Best regards


ChemAxon d51151248d

27-04-2015 08:36:57


The best solution for your problem would be to use our cxcalc command line tool to generate the lowest energy conformer. You can't select the lowest energy conformer that comes from molecular dynamics.

Use the 

cxcalc leconformer -h

command to get started. 

I hope this helps.