I started using the SD format instead, and it fixed my problems (the
molecules now have correct bond orders and they are MMFF94 optimized
properly).
Thanks for the help!
On Thu, Nov 2, 2017 at 3:21 PM, Paolo Tosco wrote:
> Hi Patrick,
>
> I don't know Avogadro in detail, but as it is based on O
Hi Patrick,
I don't know Avogadro in detail, but as it is based on OpenBabel I can
imagine it uses an algorithm to guess bond orders from bond distances,
angles, etc., whereas the RDKit does not. In fact, if I convert a
benzene ring from SMILES to SDF through PDB format (which does not
contai
Yes, that is probably correct. I am loading a pdb file for the initial
conformer, so bond orders are not specified.
But I find it strange, still, that when I use MMFF94 in Avogadro to
optimize it, it results in a planar shape even though all the bonds are
still single.
On Thu, Nov 2, 2017 at 2:38
Dear Patrick,
my guess is that you loaded the caffeine coordinates from PDB, or anyway
from a format where bond orders were not specified. All atoms appear to
be sp3-hybridized, which results in the wrong geometry being generated.
Hope that helps,
Paolo
On 11/02/17 18:20, Patrick Avery wrot
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