[Dock-fans] Fwd: Help regarding docking

Trent E. Balius tbalius at aol.com
Thu May 25 10:12:58 PDT 2017



-----Original Message-----
From: Trent E. Balius <tbalius at aol.com>
To: dinesh.konka <dinesh.konka at ahduni.edu.in>
Sent: Thu, May 25, 2017 10:11 am
Subject: Re: Help regarding docking



 I would recommend compiling DOCK6 with MPI and then submitting one multiprocessor job to your cluster.  MPI dock6 will distribute the molecules to each node for you and will gather the data for you.  

See the following for help: 

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#CommandlineArguments
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ParallelProcessing

http://ringo.ams.sunysb.edu/index.php/2017_DOCK_tutorial_1_with_PDB_4QMZ_NEW#VI._Virtual_Screening
http://ringo.ams.sunysb.edu/index.php/2017_DOCK_tutorial_1_with_PDB_4QMZ_NEW#VI._Virtual_Screening
http://ringo.ams.sunysb.edu/index.php/DOCK_Tutorials 

 
I hope that this helps,

Trent


======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: Dinesh Konka <dinesh.konka at ahduni.edu.in>
To: tbalius <tbalius at aol.com>
Sent: Wed, May 24, 2017 10:17 pm
Subject: Help regarding docking





​D​ear Sir,





I would like to introduce myself K.Dinesh from Ahmedabd university working as lab coordinator and also doing my PhD in the area of Alzheimer's disease. 


I have a small query regarding dock6. I have a database with almost 10K molecules that needs to be docked using dock6. I would like to know the protocol for the same that how can i dock all the 10K (may be in set of 100 molecules).


After docking, how can i compile my results.


With kind request, if you can help me in this, it would be a great help for my PhD.


Awaiting for a positive reply




-- 











Thanks & regards
K. Dinesh
Lab Coordinator,

Division of Biological & Life Sciences 

(Formerly, Institute of Life Sciences) 

School of Arts & Sciences,
Ahmedabad University,
Central Campus, Navrangpura, 
Ahmedabad, Gujarat-380009


Phone: +91 9898041982












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