Now i have the following problem using obminimize.
If i use: obminimize [-ff forcield] [-algorithm] <filname> to calculate the minimized energy of a given ligand a don't always get the same results. (of course I only compare results of the same ligande, calculated by the same forcefield and with the same algorithm with each other)
For some ligands it works to get the same result if I use the command above to get the same result for the minimization.
But for most of the ligands the results are not reproducible. It also depends on the ligand which forcefields deliver reproducible results.
Then I have a second question which is about obconformer.
If I use obconformer to generate a new conformation of my Ligand:
it shows me that the best of the 250 randomly generatet conformation has an energy at somewhere about 3.5 kcal/mol but after the minimization of this conformation the energy converges at about 68.2 kcal/mol.
How is this possible? I think the minimization Step should lead to e deeper energy then the one of the best generated confomer?
I already postet this Questions yesterday, but I'm not sure if I already had subscribed the mailing list by then.
So if you get this questions twice just forgett one of them.