ADL: Set Number of Torsions with scripts

Sarkis Dallakian dallakyans at gmail.com
Sat Mar 26 08:51:25 PDT 2016


Dear Dinler,

You are welcome. Good question. Check out the PrepareLigandMol function at
https://sourceforge.net/p/pyrx/code/HEAD/tree/PyRxDev/PyRx/vsModel.py#l307

It uses AD4LigandPreparation function from
AutoDockTools.MoleculePreparation, the same function used in
prepare_ligand4.py. It set sets limit_torsions based on PyRx user
preferences. If you know how to read and write Python code, you can copy
and modify it to suit your needs.

Dinler Antunes wrote
Dear Sarkis,

Thank you for the reply. I know that PyRx is an easy to use interface to
prepare docking files and run virtual screening. For the application I have
in mind I need to generate the input files automatically, using bash
scripts or python codes (in a server). It is possible to use PyRx to
generate the input files for docking without using the graphical interface?


2016-03-13 14:00 GMT-05:00 <[hidden email]
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> Message: 1
> Date: Sat, 12 Mar 2016 16:18:31 -0800
> From: Sarkis Dallakian <[hidden email]
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> Subject: Re: ADL: Set Number of Torsions with scripts (Dinler Antunes)
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>
> Dear Dinler,
>
> You can use PyRx to automatically generate pdbqt files with fixed number
of
> active torsions, regardless of the total number of bonds in the input
pdb.
>
> http://pyrx.sourceforge.net/blog/91-pyrx-07
>
> I think this still works in the 0.8 version that you can get for free
(like
> in free beer) from SourceForge. I no longer support the free version, but
> you can get excellent support and many more exiting new features in the
> latest paid version.
>
> Cheers,
> Sarkis
>
> --
> http://google.com/+SarkisDallakian
>
> On Sat, Mar 12, 2016 at 12:00 PM, <[hidden email]
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wrote:
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> >    1.  Set Number of Torsions with scripts (Dinler Antunes)
> >
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> > Message: 1
> > Date: Fri, 11 Mar 2016 14:10:07 -0600
> > From: Dinler Antunes <[hidden email]
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> > Subject: ADL: Set Number of Torsions with scripts
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> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear fellow subscribers,
> >
> > I am running some experiments with peptide ligands and I want to run
> > several dockings with ligands with different sizes, but always sampling
a
> > small subset of the total amount of (possible) flexible bonds. The
> optional
> > feature "Set Number of Torsions" available in ADT would be perfect for
> this
> > task. I just want to provide the ligand and the number of bonds to be
> > flexible (let's say 6), and get a pdbqt file with TORSDOF 6. At this
> point
> > doesn't matter to me which bonds are being sampled. However, I want to
do
> > this in an automated way (script) and prepare_ligand4.py doesn't seem
to
> > allow to "set the number" of active torsions (without providing a
> specific
> > list of atoms with -I). There is any way of automatically generating a
> > pdbqt file with a fixed number of active torsions, regardless of the
> total
> > number of bonds in the input pdb?
> >
> >


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