ADL: +ve docking energies

Raj Badhan mophlrkb at
Fri Feb 11 02:13:51 PST 2005

Dear Users,

We are docking a series of flavonoids into out site and have come across a
stumbling block with a compound called Chalcone.

This is a flavonoid with only ONE carbonyl oxygen and no other functional

We have been able to use PRODRG to assign charges and convert the small
molecules to PDBQ format with much success, however, with this one compounds
we ALWAYS get +ve binding energies.

Experimental studies has shown interactions, so maybe the compound binds
elsewhere? But we are sure it doesn't.

We have tried minimising energies elsewhere and using prodrg to just convert
to PDBQ but again, to no avail.

Any suggestions would be helpful.

Raj Badhan

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