Hi All!
I got 2-3 messages on ModelBuilder 3D and I do think it would be
good to designate the package as deprecated as it fails in many
cases.
I would also like to share a bug : in many drug-size molecules the
builder assigns bad MMFF94 atom types to the amide Ns, which results
in bad 3D geometry, namely neglecting the amide plane. It works well
in cases when the amide in like NC=OR, where R is alkyl group, but fails
when the first R atom is not C. Therefore in cases like urea, hydroxyurea
the result is bad.
The problem was in MMFF94BasedAtomTypePattern where you have to change the
N atom HOSECODE pattern
N-[1-3];[CH]{1,3}.{1}+[A-Z]{0,3}+[,]?+=OC.*+
to
N-[1-3];[CH]{1,3}.{1}+[A-Z]{0,3}+[,]?+=O[CNX].*+
to handle other types of amides.
How can I report this bug ?
Thanks, Daniel
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