Thank you Oliver =)
I managed to get it running. I will appreciate feedback from David on docking of gags
From: Oliver Grant
Sent: Tuesday, 19 September, 19:04
Subject: Re: 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.
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
Is there an example of docking using Vina-Carb?
Sent: Tuesday, 19 September 2017 4:17 PM
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?