Subject: Re: CCL:question about autodock

From: Christian Pilger <[email-masked]>
Date: Sun, 6 Jun 1999 11:58:10 +0200

On Sat, 5 Jun 1999, maoxiang wrote:

> Hi, everyone:
>    I am an new man in the CCL. 
>    Here is a question I wish you can help me. I am using AUTODOCK(ver
> 2.4) to dock my ligand, but I find almost all of the result of the
> position of ligand have bumps with the receptor. Does someone have met
> the problem in the work, maybe there are some mistakes in my setup. Hope
> to hear from you soon.
> 
> 
> With best regards,
> Mao Xiang
> 

Dear Mao Xiang,

	we obtained similar results with AutoDock. I think one cause may
be the grid-spacing you enter into AutoGrid (by default: 0.375 A). If you
decreased the distance between the grid points I would expect you to get
better energies and less bumbs. However to overcome this problem and at 
the same time the problem of receptor rigidity we used a different force
field (i.e. TRIPOS) to achive some "fine-tuning" of the ligand-enzyme-
alignments suggested by AutoDock. The applied force field distinguished
more atom types than AutoDock does and additionally allowed us to keep
those amino acid residues flexible, that were flanking our proposed
binding site ("induced fit").

Regards,

Christian

-----------------------------------------------------------------

 Dipl.-Chem. Christian Pilger          Uni-GH Paderborn
                                       FB 13 - Organische Chemie
                                       Warburger Str. 100
                                 
                                       D-33098 Paderborn/Germany
 Tel.: 05251-60279/-602183         
 Fax : 05251-603245         email: [email-masked]

 Word Wide Web: 	   http://oc30.uni-paderborn.de/~cpilger
 
-----------------------------------------------------------------