ADL: Set Number of Torsions with scripts

Dinler Antunes dinler at gmail.com
Fri Mar 25 13:58:57 PDT 2016


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 <autodock-request at scripps.edu>:

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>    1. Re:  Set Number of Torsions with scripts (Dinler Antunes)
>       (Sarkis Dallakian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 12 Mar 2016 16:18:31 -0800
> From: Sarkis Dallakian <dallakyans at gmail.com>
> Subject: Re: ADL: Set Number of Torsions with scripts (Dinler Antunes)
> To: autodock at scripps.edu
> Message-ID:
>         <
> CAAWj0RAxEOAfpXvoeUDywYJDC6mJD3SG75NSDimo+hNa128sRg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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, <autodock-request at scripps.edu> wrote:
>
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> > Today's Topics:
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> >    1.  Set Number of Torsions with scripts (Dinler Antunes)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 11 Mar 2016 14:10:07 -0600
> > From: Dinler Antunes <dinler at gmail.com>
> > Subject: ADL: Set Number of Torsions with scripts
> > To: autodock at scripps.edu
> > Message-ID:
> >         <
> > CAEjxMVgEv15VV0i6wdfBin1hOqiz7H0puD+pQK5rxUaWor+iSA at mail.gmail.com>
> > 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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-- 
Dinler Amaral Antunes


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