Hi Neha,

Here's the instructions for installation: 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.



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

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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,