I have recently started using screen3d to preform structure comparisons, and have been getting the message:
Aug 18, 2014 8:27:45 PM chemaxon.marvin.alignment.AlignmentBase optimization
INFO: Optimization was not converged.
How can I avoid this? It is only happening for about half the structures I am screening, but it has me stumped! can I increase the time allowed, or would this help?
I am using screen3d as follows:
screen3d s -t ncidiv.ser -q Abacavir.ser frq
Where ncidiv.ser is a list of ~1600 structures. Would it be possible to view which structure is throwing the errors so that it may be examined or removed?
OS: 64 bit linux
Thank you in advance! Your tools have been indispensable.