[Dock-fans] DOCK 6 amber scoring

Floris Buelens floris_buelens at yahoo.com
Tue Oct 10 07:13:20 PDT 2006

Hi, regarding your second point, I made a quick and dirty perl script that does what you're looking for. Specify the scored mol2 file, and it looks for a series of files names *xx.final_pose* - if it finds what it expects - i.e. a certain number of molecules in the mol2 file and an equal number of final_pose pdb files, it'll write out a file ending ".mod.mol2" with the new co-ordinates. Hope that works for you!
Best of luck

----- Original Message ----
From: Jeffrey Dyason <j.dyason at griffith.edu.au>
To: Dock-fans at docking.org
Sent: Monday, 9 October, 2006 6:05:06 AM
Subject: [Dock-fans] DOCK 6 amber scoring

I'm just starting to play around with the Amber scoring module in DOCK6 
and I have a few problems. I've updated and recompiled DOCK6 with the 4 
patches available and it seems to run fine on my Mac running MacOSX 
10.4.8. The first problems arose from the mopac.sh script which requires 
the DOCK_HOME to be set, easily fixed but it wasn't mentioned in the DOCK 
6.0 User manual. 
Secondly, the mopac.sh script uses the following line :-
ln  mopac.in FOR005
on my mac this doesn't work. It needs to be 
ln -s mopac.in FOR005

When, I have run an Amber scoring calculation I just allow the ligand to 
be flexible, with the protein fixed and everything thing seems to work 
fine, except for the output coordinates. The file 
protein.ligand.1.final_pose.pdb has the ligand coordinates updated, 
however the other file that is written out output_scored.mol2 only has the 
starting coordinates (plus the updated score). Is it possible to get the 
updated ligand coordinates to be written to output_scored.mol2 file ? 
Also, is it possible to get the final coordinates of the ligand by itself, 
after it has undergone the dynamics, to compare with the docked structure 

Thanks Jeff.
Jeff Dyason                                    e-mail: 
J.Dyason at griffith.edu.au
Institute for Glycomics http://www.griffith.edu.au/glycomics
Griffith University                          (Gold Coast Campus)  
PMB 50 Gold Coast Mail Centre       Tel: +61 7 5552 7028
Queensland 9726 Australia              Fax: +61 7 5552 8098
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