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 Post subject: generate pdbqs
PostPosted: Wed Feb 19, 2014 3:45 am 
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Hi all,
I was trying to generate the pdbqs file using AutoDockTools-1.5.7. But, when I write a pdbqs file, it tells me that all atoms do not have a solvation fields. Then, I read, solvation fields can be added by Grid->Macromolecules ->Add solvation Parameters, but when I go to Grid -> Macromolecules, I didn't see the option of Add solvation Parameters. Then, I also tried File -> Browse Commands -> select the module (autogpfCommands) which has ADgpf_addSolvationParameters. But, still, I didn't see the option of Add solvation Parameters under Grid -> Macromolecules.
Any suggestions of how to generate the pdbqs file? Thank you so much!

Best,
Wei


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 Post subject: Re: generate pdbqs
PostPosted: Thu Feb 20, 2014 10:34 pm 
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To create a pdbqs file for use with autodock3 (the older version of autodock) use the script "prepare_receptor.py" ( in MGLToolsPckgs/AutoDockTools/Utilities24 directory) .

Here's how:
In the MGLToolsPckgs directory on your computer, invoke the script like this:
../bin/pythonsh AutoDockTools/Utilities24/prepare_receptor.py -r hsg1.pdb -A hydrogens -o hsg1.pdbqs

Note: the latest versions of autodock (4+) use pdbqt format input for both the receptor and the ligand...


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 Post subject: Re: generate pdbqs
PostPosted: Sat Feb 22, 2014 5:07 pm 
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Thank you so much!
But, I am wondering how I can invoke the script you mentioned. Could this be done somewhere in AutoDockTools GUI window?
'../bin/pythonsh AutoDockTools/Utilities24/prepare_receptor.py -r hsg1.pdb -A hydrogens -o hsg1.pdbqs'

And, when I opened MGLTools-1.5.4 packages, I only saw AutoDockTools-1.5.4, PMV-1.5.4, Update Manager-1.5.4, Vision-1.5.4, and if I show package contents for AutoDockTools-1.5.4, I still didn't see Utilitites24 directory.

Thank you so much!

Best,
Wei


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 Post subject: Re: generate pdbqs
PostPosted: Sun Feb 23, 2014 11:48 pm 
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"....Could this be done somewhere in AutoDockTools GUI window?"
No, you can't invoke the script from the AutoDockTools GUI window...

INSTEAD you must open a terminal [and if necessary, change directory to your local MGLToolsPckgs]
THEN type the following in the new terminal window:
'../bin/pythonsh AutoDockTools/Utilities24/prepare_receptor.py -r hsg1.pdb -A hydrogens -o hsg1.pdbqs'

Note:
-AutoDockTools is a sub-directory of MGLToolsPckgs
-Utilities24 is a sub-directory of AutoDockTools

BTW: AutoDock3 used 'pdbqs' file format for the receptor and pdbq for the ligand.
The newer version "autodock4" uses 'pdbqt' format for both the ligand and the receptor...
?Are you sure you want to use autodock3?


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 Post subject: Re: generate pdbqs
PostPosted: Mon Feb 24, 2014 12:39 am 
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Thank you so much! What I am trying to do is to estimate the binding energy of X-ray protein-ligand complex structure. I am using AutoDockTools-1.5.7. I don't whether I need pdbqs file.... But, since I read from a literature (RYANGGUK KIM, JEFFREY SKOLNICK, 2007) saying that:
'The receptor structure files were converted to pdbqs format with pmol2q40 and used as the input files. The ligand structure files were processed with AutoDockTools to produce pdbq format input files. Grids of length 30.0 A were placed around the center of ligands with a spacing of 0.375 A . The gpf and dpf parameter files were generated with gpf3gen and dpf3gen provided in the AutoDock package, respectively. The binding energy evaluation was performed with epdb command on the native receptor and ligand structures.'

I am wondering whether the above description is the way how binding energy is estimated in AutoDockTools-1.5.7. If so, I am wondering how I could or where I could find more information on how to generate gpf and dpf parameter files and run epdb command in AutoDockTools-1.5.7.

Thank you so much!

Best,
Wei


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 Post subject: Re: generate pdbqs
PostPosted: Mon Feb 24, 2014 4:14 pm 
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Look at the AutoDock UserGuide:
http://autodock.scripps.edu/faqs-help/manual

It includes theory as well as detailed instructions for creating input files, running the number-crunching calculations and analyzing the results.


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