[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:


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.


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

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