Fw: Re: [Dock-fans] several basic questio n!

Sudipto Mukherjee sudmukh at yahoo.com
Thu Oct 12 19:51:09 PDT 2006


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

 


 

 

 

 

 

 

 




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·¢ËÍʱ¼ä:2006-08-25 07:37:26
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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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