ADL: Autodock4 - Queries.

Remya Francis M. remyafrancis at gmail.com
Wed Jan 9 22:37:38 PST 2008


Dear Sir,

 I have some doubt in Autodock4 command line running. My work will be
complete only after to clear this doubt. So please help me for clear my
queries.

*(1)* How can i select *simulated annealing(SA)* algorithm in 'docking
parameter file step' using command line?

>pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1.pdbqt

this command help to use default lamarckian genetic algorithm(LGA) for
docking


 >pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1.pdbqt -L -o LS_L.dpf

this command help to use local search(LS) algorithm for docking


 > pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1.pdbqt -o GA.dpf -p
do_global_only=50 -p ga_run=0

this command line output(.dpf file) help me to select 'Genetic Algorithm' in
the autodock step.


How can i select simulated Annealing algorithm separately? I am not able to
find any supporting document also. Please help me in doing this.


 *(2)* In the a Docking parameter file preparation step, have '-k' option
for specify the 'list of parameters to write'.

How '-k' option is used in command line? Whats its important? The usage or
description about this option is not provided.


 *(3) * In the grid parameter file preparation step have '-d' option for
specify the 'directory of ligands to use to set types'.

What does '-d' option mean in detail?. Does it mean for specify the multiple
ligand directory?.


 I tried following commands

>pythonsh prepare_gpf4.py -l ind.pdbqt -r hsg1.pdbqt

i got correct output for this command.


 > pythonsh prepare_gpf4.py -l ind.pdbqt -r hsg1.pdbqt -o hsg1_d.gpf -d
/root/Desktop/AUTODOCK4/Testing_cmd/Grid-3 /pdbqt

/root/Desktop/AUTODOCK4/Testing_cmd/Grid-3 /pdbqt -> this directory contains
3 ligand files with .pdbqt format.

output (hsg1_d.gpf) file haven't no information about 'ligand_types' and
'map files'

*********************** hsg1_d.gpf**********************

npts 42 40 40 # num.grid points in xyz

gridfld hsg1.maps.fld # grid_data_file

spacing 0.375 # spacing(A)

receptor_types A C N NA OA SA # receptor atom types

ligand_types # ligand atom types

receptor hsg1.pdbqt # macromolecule

gridcenter auto # xyz-coordinates or auto

smooth 0.5 # store minimum energy w/in rad(A)

elecmap hsg1.e.map # electrostatic potential map

dsolvmap hsg1.d.map # desolvation potential map

dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant

****************end of hsg1_d.gpf**********************


 How can i use '-d' option?. Please give me one command line example with
this option. No where in the document give its usage.

If '-d' option is not for specify the multiple ligand directory, then how
can i dock multiple ligand with one receptor? Is it need to run each script
for each ligand?. Or in autodock4 have any single script/command for run
multiple ligand ?

I am waiting for your response.


 With Thanks & Regards,

Remya Francis M.


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