ADL: Question about AutoDock tools!

Richard Wood Richard.Wood at
Sat Mar 5 07:37:00 PST 2016

I am sure if you go to, there is something that will help you there.

From: autodock-bounces at [autodock-bounces at] on behalf of sandra [sandra at]
Sent: Thursday, March 03, 2016 2:35 PM
To: autodock at
Subject: Re: ADL: Question about AutoDock tools!

Hey thank you for this response, Richard. I was wondering if you could
possibly guide me towards decent tutorials on using Marvin Sketch,
specifically conformational distriution for a 3D model of a small ligand
(such as the D-isomer of ETH-LAD)? Thank you very much :) Cheers.

On 2/25/2016 3:36 PM, Richard  Wood wrote:
> Actually, you could use ChemAxon's MarvinSketch to sketch molecules in 3D and save them in any format you wish.
> Marvin is free.
> Richard
> ________________________________________
> From: autodock-bounces at [autodock-bounces at] on behalf of sandra [sandra at]
> Sent: Wednesday, February 24, 2016 4:31 PM
> To: autodock at
> Subject: ADL: Question about AutoDock tools!
> Hi there! I am a McMaster student and I am looking to use AutoDock Tools
> and the Grid interface for some academic research as a student. I
> encountered an error while using it and I was wondering if I could
> possibly ask some questions. I apologize if these questions are overly
> lengthy or too simplistic to you as I am just a beginner.
> I used a model of the 5HT-1B human peptide receptor, crystallized with
> the ligand ergotamine. Its codename in RCSB is "41AR". I want to replace
> ergotamine with a different molecule, such as LSD, and dock it.
> I used AutoDock Tools to select the molecule ergotamine, and then delete
> its space. There is an empty gap left where it was docked. There is an
> additional molecule in the model, I believe tartaric acid. Anyways, I
> left the tartaric acid in because I figured LSD is also a hemi-tartrate
> salt, like ergotamine.
> Anyways, I followed this video guide on AutoDock Tools
> ( because like my project,
> it is using a crystallized receptor model (not a homology-modeled one)
> in pdb format obtained from RCSB, is introducing a separate ligand as a
> PDB file, and uses Windows 8 (i am using Windows 10 for my project).
> I followed the steps: delete all water molecule, add all hydrogens (both
> polar and nonpolar), merge non-polar hydrogens, computer partial
> Gasteiger charges, and then I selected Input>Ligand>Select. I added in a
> .pdb file for LSD; I couldnt find a ligand file for LSD on the RCSB, so
> instead, I drew it out as a simply 2D sketch (in the d-siomer form) on
> ACD ChemSketch (freeware version),  saved it as a .mol file (v3000), and
> then I used OpenBabel to convert the v3000 .mol file into a .pdbqt file,
> as suggested in the tutorial vid.
> However when I attempted to load it, it could only partially model the
> ligand, and some atoms seemed to be missing. In the Python shell, there
> was an error message, which I have attached in this email as a .txt file.
> I was wondering if you would possibly be able to review over what I did
> and tell me where I went wrong? I understand my question is a bit ranty
> and rudimentary so I don't want to pressure you :P Any help however
> would be extraordinarily useful. Thank you very much!
> ________________________________________________
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