Hi there OpenBabels!
I am generating conformers for
molecule C(=O)(O)C(C)(C)Oc1ccc(cc1)CC(=O)Nc1cc(cc(c1)C)C using the
--conformer option (and --writeconformers, otherwise I get only one
conformer written to file) in the following manner :-
obabel ligand_babel3d.sdf -O conf2.sdf --conformer --nconf 50
--writeconformers
Some of the generated conformers look really ugly (in terms of close
atoms/steric clashes).
I have placed a selected subset at: http://imgur.com/a/LgJqL
Is that to be expected in RMSD scoring -- because I have not used --score
energy? (I tried the energy scoring, and the molecules look more
reasonable). Is rmsd scoring a sensible default then? Should these
molecules be removed by the algorithm in rmsd scoring?
As an unrelated sidepoint - a suggestion - is it possible to get an error
when specifying flags which do not exist? I thought I was using the
weighted rotor search option all morning but was scratching my head as to
why I was getting many conformers (instead of 1). Turns out I was typing
-weight instead of --weighted (doh!). I think this would improve the user
experience.
Many thanks on a Sunny Sunday.
-
Jean-Paul Ebejer
Early Stage Researcher
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