Hi Neha,

Here's the instructions for installation:

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:

-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]>

> 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]
> 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