Re: CCL:local search in AutoDock

Hi Robert,
 wat you are experiencing is probaly a bug in  ADT. I don't know wich version
 you are using, but try to download the last one. I had the same problem a few
 month ago and I solved it by choosing a random start, because it seemed that
 ADT didn't recognize properly the ligand starting coordinates relative to the
 receptor file; the docking run was correct but there was some sort of offset
 between the ligand conformations and the receptor. By choosing a random
 start, If everything works fine, you should be able to properly reproduce
 your docking and to correctly visualize results.
 Hope this help
 Alessandro Contini
 Alle 15:07, martedl 24 giugno 2003, Robert Flight ha scritto:
 > Hi,
 >
 > I'm trying to use a local search (pseudo-sw) to minimize a docked pose of a
 > ligand into a receptor.  When I look at the ligand and the receptor in ADT,
 > the ligand is in the correct starting position.  The Grid box is large
 > enough to contain the search space.  I'm using a non-random start,
 > non-random relative dihedral offset, and initial relative dihedrals, which
 > should all start the local search from the specified initial coordinates.
 >
 > The output ligand poses end up completely outside the docking box, and
 > outside the receptor as well, with an RMSD of 85 Angstroms!!!  Can anyone
 > tell me what is happening, as I see no reason why the ligand should end up
 > outside the docking box!
 >
 > Thank you for your help,
 >
 > -Robert
 >
 > ********************************
 > Robert Flight
 > Masters Student
 > Department of Chemistry
 > University of New Brunswick
 > Fredericton, NB  Canada  E3B 6E2
 > e-mail: robert.flight^at^unb.ca
 >
 > ********************************
 >
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 realize
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 from
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 --
 Alessandro Contini, Ph.D.
 Istituto di Chimica Organica "Alessandro Marchesini"
 Facolt` di Farmacia Universit` degli Studi di Milano
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 Tel. +390250314480  Fax +390250314476
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