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Hi Neha,

Here's the instructions for installation:
 http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/vina-carb/
<http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/vina-carb/>

Just follow the regular instructions for preparing your ligand pdbqt file
in autodock or autodock vina. I use the command line version instead of
autodock tools e.g:

/programs/e12/mgltools_x86_64Linux2_1.5.6/bin/pythonsh
/programs/e12/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py
-l ligand.pdb -Z -o ligand.pdbqt

I'm fairly confident vina-carb was not developed for GAGs though, but
*@David* or *@Spandana *are doing GAG docking, so may have a recommended
protocol and an idea of accuracy.

Best,

Oliver

On Tue, Sep 19, 2017 at 10:45 AM, Neha S. Gandhi <[log in to unmask]>
wrote:

> Further to my query, I would like to know how to prepare pdqt file for
> carbohydrates in Vina-Carb. I am downloading pdb file (heparin
> tetrasaccharide) from glycam server. Do I need to change the atom types in
> the pdbqt file to match glycam atom types prior to docking?
>
> Is there an example of docking using Vina-Carb?
>
>
>
> -----Original Message-----
> From: Neha Gandhi [mailto:[log in to unmask]]
> Sent: Tuesday, 19 September 2017 4:17 PM
> To: [log in to unmask]
> Cc: Neha S. Gandhi <[log in to unmask]>
> Subject: VIna-carb
>
> [This sender failed our fraud detection checks and may not be who they
> appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing]
>
> Dear List,
>
> I downloaded Vina-carb. I am trying to figure out its installation. Do we
> simply untar it or we have to compile from the source?
>
> Many thanks,
> Neha
>
>