I've noticed a that when building unsaturated 6-membered rings with attached groups (e.g.
"CC1CCC(C)CC1"), the result will have the groups systematically placed in axial position,
instead of equatorial.
I've tried looking into it to propose a possible solution, but I couldn't pin exactly
where this happens in the code.
I know that the ring conformation is built from the fragments.txt, but it that file there
isn't any information about atoms other than those constituting the ring (as far as I can
tell).
I suspect the problem might be in builder.cpp, where the math for the bond angles is
computed, but where exactly I have no idea.
The issue becomes a problem when there are more than a handful of molecules to process,
because geometries must be corrected by hand (unless there is an ob.method that can be
used for that).
Any insights on how to deal with it?
Thanks,
S
--
Stefano Forli, PhD
Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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