Thank you David. Last question is did you use the chi energy function or the coefficient cut-off for docking and scoring of gags?

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From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of David Thieker <[log in to unmask]>
Sent: Wednesday, September 20, 2017 12:38:56 AM
To: [log in to unmask]
Subject: Re: VIna-carb
 
I normally use the ADT GUI, but it's quite slow, so I just tried the command line protocol that Oliver suggested. It works, but I recommend leaving off the '-Z' option, which restrains all of the torsions (including hydroxyl orientations). By default, all rotatable bonds are active except for amide and guanidium.

Autodock Vina (and therefore Vina-Carb) does not include a scoring term for electrostatics, simply relying on a hydrogen bonding term. As a result, the program has a difficult time with blind docking, or choosing where the binding site should be on the protein surface. However, if you already have a good idea of where the ligand binds (i.e. alanine scanning, near the catalytic residue, etc.), Vina-Carb can produce accurate models. It helps if you have a positive control.

For example, I successfully docked the substrate within the co-crystal of an enzyme (PDB ID: 4NDZ) back into the protein with an RMSD of the recognized trisaccharide (GlcNS-IdoA-GlcNS) of < 1 Angstrom. This gave me confidence in using the program on the same enzyme, with the same settings, in order to predict the binding mode of alternative ligands.

Due to the large number of rotatable bonds, as well as the size of the grid box that is often required, you should try increasing the exhaustiveness within the config file. The default is 8, so I used 80 in the example described above.

Please let me know if you have any other questions.

Best,
David

On Tue, Sep 19, 2017 at 5:07 AM, Neha S. Gandhi <[log in to unmask]> wrote:
Thank you Oliver =)
I managed to get it running. I will appreciate feedback from David on docking of gags

Cheers,
Neha

From: Oliver Grant
Sent: Tuesday, 19 September, 19:04
Subject: Re: VIna-carb
Hi Neha,

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
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,
Neha







--
David F. Thieker
PhD Candidate
Biochemistry and Molecular Biology
Complex Carbohydrate Research Center
University of Georgia, Athens, GA