[Dock-fans] DOCK3.6 output broken compounds, hydrogen and sulfur swap

Yi Shang mirandaisbest at gmail.com
Fri Dec 12 14:55:24 PST 2014


Hi All,
I am having some weird broken compounds in my topdock.py pdb output. And
they seem to contain specific functional groups like O=S=O.

For example
https://dl.dropboxusercontent.com/u/76890735/trouble.pdb  is one of the pdb
output that seems to have one sulfur and one hydrogen swapped in 3D
coordinates.

https://dl.dropboxusercontent.com/u/76890735/21_0.265.db.gz  is the
flexible database downloaded from ZINC, which contains the that compound
above.

https://dl.dropboxusercontent.com/u/76890735/zinc_2804795.ddb is db format
file for the same compound that I downloaded directly from ZINC. It matches
21_0.265.db.gz, so I think the pdb problem happens after DOCK3.6 reads in
21_0.265.pdb.gz.

Does anyone have any experience with this?

Thanks!

-- 
Yi  Shang,   Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
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