[Dock-fans] rigid bonds

Jean DESSOLIN j.dessolin at iecb.u-bordeaux.fr
Thu Mar 22 00:50:28 PST 2007

Dear Dockers,

I have been using Dock 5.4 for a while now, and there is a feature I 
still cannot comprehend. Thus I'm truning to the community to check if 
someone has a hint about what to do.

I am docking small molecules that contains amide bonds, some are 
peptides, some are not. I'm preparing my database with InsightII, saving 
the ligands as mol2 files.
With InsightII, I define the amides as partial double bond between the 
carbon and the amide, and this bond is defined as 'ar' by the soft in 
the @<TRIPOS>BOND. When running dock, many time I get a dihedral angle 
between 100 to 180 degrees. Ok, 180 is what one expect, but the 
possibilities between both values are not expected. After checking the 
Dock web site, I found out that the link could be defined as 'am' 
instead od 'ar', I still get torsions with the amide bonds. Same thing 
if I define it as double bond ('2' instead of 'ar').
After careful reading of the manual, I tried to define as STATIC BOND 
SET the amide bond(s), by writing by hand in the mol2 file. Guess what, 
I still get the same result, with a torsion on the amide, and the 
written output mol2 files does not contain anymore the rigid set I imposed.

Does anybody know how to overcome this ?

Many thanks to contributors.


j.dessolin at iecb.u-bordeaux.fr
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
Tél : 33 (0)5 40 00 30 29
Fax : 33 (0)5 40 00 22 15

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