[Dock-fans] several basic questio n!

Philip Crawford p.crawford at unsw.edu.au
Thu Oct 12 20:57:43 PDT 2006


Fralium, Sudipto,
If you screen only the remainder of the database, you won't have the first set included in the Ranked Output file.
If you want to screen the remainder of the database and are recording Output conformations.
 
do a 
grep -c "MOLECULE"
on the conformations database. This gives you a count of how many molecules have been screened.
 
You can then restart with basically the same dock.in file, except that you need to set:
initial_skip        Count_from_grep_command
(If running MPI Dock, I'd recommend subtracting the number of processors you are using from that count. I guess, however, that you are only running one.)
 
One issue with running batches of small databases is combining and sorting the results.
 
Dock Team:
It would be a nice feature if Dock could write out a ranked_output.mol2 file after, say, every 1000 molecules, with a count of how many molecules have been scored at that point. This would prevent loss of results from crashed jobs and consequent reprocessing.
 
Phil
__________________________________________________
Philip Crawford, B. Comp. Sc., MIEEE
School of Medical Sciences
The University of NSW
Phone: +61-2-9385 2564
Mobile: +61-419-294 698
Fax: +61-2-9385 1059
Email: p.crawford at unsw.edu.au
__________________________________________________
 

  _____  

From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org] On Behalf Of Sudipto Mukherjee
Sent: Friday, 13 October 2006 12:51 PM
To: DOCK Fans Mailing List
Subject: Fw: Re: [Dock-fans] several basic questio n!


Fralium,


Dock6 does not have a restart file. However, you might be able to avoid re-screening the ligands that finished. Checking the dock.out file to see how many ligands finished, and create a new database with the remaining unscreened ligands. 

Consider breaking up large databases into smaller chunks (~10,000 ligands each), and running dock on each chunk separately. This reduce the memory usage, and also ensure that an unscheduled restart or crash will not hurt too much. 

Regards
Sudipto


----- Original Message ----
From: fralium <fralium at 163.com>
To: sudipto mukherjee <sudmukh at yahoo.com>
Sent: Thursday, October 12, 2006 5:07:17 AM
Subject: Re: Re: [Dock-fans] several basic questio n!


Hi,Sudipto
 
  Sorry to bother you again!
  I met a little problems in using the dock6!can you help me?
  i was screening a database,but the machine restarted,must i restart too?can i continue the calculation before the restart?
 
  Thank you!
 
Regards
 
                                                                fanglei
 
 
 
 
 
 
 
 

  _____  


-----ԭʼÓʼþ-----
·¢¼þÈË:"Sudipto Mukherjee" 
·¢ËÍʱ¼ä:2006-08-25 07:37:26
ÊÕ¼þÈË:"fralium" 
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Ö÷Ìâ:Re: [Dock-fans] several basic question!



Hi Fralium,

Congratulations for choosing DOCK6!
To answer your questions:

1,Is it necessary to minimize the ligand (already add hydrgon,charges)(and this ligand is extracted from the complexity)  before docking? and if I change the sturcture of it ,such as i change the phenyl with methyl? minimize? Will this change its coordinate? 

DOCK has its own built-in minimizer, so minimizing the ligand prior to docking is not strictly necessary. In this case, I would recommend you enable flexible ligand so that DOCK will change the ligand torsions during docking. 

It is necessary to add hydrogen atoms and assign partial charges in order to dock the ligand. 
Further, changing the ligand structure will most certainly change it's coordinates.

   2,If I intend to do flexible docking ,how to define the ANCHOR and RIGID set in SYBYL7.1? I mean is there any more information than I can get from the dock manul? Can anybody give me some systemic information?

You do not need to define the anchor or the rigid set in SYBYL Anchor assignment occurs automatically during docking. In order to dock a ligand, you will need just the protonated ligand MOL2 file with partial charges. 

Regards
Sudipto Mukherjee


----- Original Message ----
From: fralium <fralium at 163.com>
To: dock-fans at docking.org
Sent: Wednesday, August 23, 2006 7:26:33 PM
Subject: [Dock-fans] several basic question!


Dear everybody,
 
   I'm a new learner of DOCK 6,now I have several question about it!
 
   Thank you for all your information!
   1,Is it necessary to minimize the ligand (already add hydrgon,charges)(and this ligand is extracted from the complexity)  before docking? and if I change the sturcture of it ,such as i change the phenyl with methyl? minimize? Will this change its coordinate? 
 
   2,If I intend to do flexible docking ,how to define the ANCHOR and RIGID set in SYBYL7.1? I mean is there any more information than I can get from the dock manul? Can anybody give me some systemic information?
 
 
   That's all.Thank you again!
 
yours
 
                                                                 fralium
 
                                                                   GUCAS
 
 
 








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