ADL: Set Number of Torsions with scripts (Dinler Antunes)

Sarkis Dallakian dallakyans at gmail.com
Sat Mar 12 16:18:31 PST 2016


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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>    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 <dinler at gmail.com>
> Subject: ADL: Set Number of Torsions with scripts
> To: autodock at scripps.edu
> Message-ID:
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> 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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