ADL: Doubt in 'docking parameter file preparation step'.

Remya Francis M. remyafrancis at
Mon Jan 7 03:36:55 PST 2008

Hello  Sir,

I am Remya Frsnics M, Delhi. Working in a Bioinformatics company.

Sir, Now i am working in Autodock4(Command line). I have some doubt on it.

I am stuck in the 'docking parameter file preparation step'.

(1) How can i select one algorithm using command line?

" *pythonsh -l ind.pdbqt -r hsg1.pdbqt -o
Local_Search_Algo.dpf -L* "

-L helps me in specifying only LocalSearch algorithm

if i do not define anything then by default LGA is working

i want to run docking only with simulated anealing or with genetic algorithm
or with local search or with LGA. In this case i know how to run only LGA
and Local Search but how to go separately for other two i am not able to
specify. I am not able to find any supporting document also. *Please help me
in doing this.*

 (2) How can I use "-k" option in the 'docking parameter file preparation

 With Thanks & Regards,

Remya Francis M.

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