Hello,
I am trying to alter only the torsion angles of a molecule when e.g.
minimizing or generating conformers. When just calling e.g. SteepestDescent
or RandomRotorSearch of the OBForceField class, I noticed that also bond
lengths and bond angles were changed. I then tried using the OBFFConstraints
class to constrain all bond lengths and bond angles to their original
values. That helped, but I still saw slight changes (e.g. a bond length
constrained to 1 could become 1.003). Then I (by chance) tried to use
the SetFactor method with different values and I found out that constraints
were more likely to be respected completely (the processing time also
increases) if I used SetFactor with a high value before adding any
constraints. Can anybody explain to me if this is correct?
I found out about the methods using the API at [1] and [2] and played a bit
with them. Disclaimer: I am a computer scientist, not a biochemist or
anything like that.
I am using Open Babel 2.3 via the Java wrapper.
[1] http://openbabel.org/api/2.3/classOpenBabel_1_1OBForceField.shtml
[2] http://openbabel.org/api/2.3/classOpenBabel_1_1OBFFConstraints.shtml
Regards,
Martin.
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