[Dock-fans] Short contact in ligand

Carlos P Sosa cpsosa at msi.umn.edu
Wed May 27 09:11:25 PDT 2009

Hi Rahul,

You need to check with Prof Rizzo's group at Stony Brook, they have a
developmental version that overcomes this problem.  I believe that Sudipto
(one of Prof Rizzo students) posted a message about this problem a couple
of weeks ago.

> Hi,
> Sometimes I am getting very strange geometries of the ligand in Dock run.
> Two groups or atoms in the ligand are in short contact. Cases are even
> worst if I use use_clash_overlap . If I don't use use_clash_overlap there
> is marginal improvement. Is there any other option I can use to get rid of
> these highly strained ligand conformations? I am using grid based scoring
> to screen big databases. I some cases ligands with these type of strained
> geometries are appearing among top ranked compounds.
> With best regards,
> Rahul Banerjee
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