[Dock-fans] How to score a single pose

Trent E. Balius tbalius at aol.com
Mon Apr 2 19:10:30 PDT 2012


 Hi Brad,

DOCK reads in mol2 files.

The ligand and receptors must be in separate mol2 files (lig.mol2, rec.mol2).

You may wish to use a program like chimera to process the PDB file into these two mol2 files

To perform a single point calculation use the following set of input parameters:

ligand_atom_file                                           lig.mol2
orient_ligand                                                no
flexible_ligand                                              no
score_molecules                                          yes
contact_score_primary                                  no
continuous_score_primary                             yes
cont_score_rec_filename                               rec.mol2 
minimize_ligand                                            no

See the following as well:

http://mailman.docking.org/pipermail/dock-fans/2008-October/001754.html

I hope this helps,

Trent E. Balius
Graduate Student, Rizzo Group
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Brad Ridder <clustro at gmail.com>
To: dock <dock-fans at docking.org>
Sent: Mon, Apr 2, 2012 9:38 pm
Subject: [Dock-fans] How to score a single pose


Hi DockFans,

Is there a simply way to feed DOCK a pdb file with the receptor + bound ligand, and have it return a score back for that pose, without doing any sort of energy minimization? e.g. just give the energy score for that single pose.

-Brad

-- 
Bradley James Ridder
Chakrabarti Group
Graduate Student
School of Chemical Engineering
Purdue University



 
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