ADL: Question about AutoDock tools!

Richard Wood Richard.Wood at purduecal.edu
Sun Mar 6 05:44:54 PST 2016


You could either save your MarvinSketch compound as a mol2 and convert it to a pdbqt using ADT, or or save teh MS as a pdb and convert the pdb using ADT.

Richard
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on behalf of sandra [sandra at theindoleshop.com]
Sent: Saturday, March 05, 2016 1:22 PM
To: autodock at scripps.edu
Subject: Re: ADL: Question about AutoDock tools!

Thank you, I was able to create a .pdb file for the ligand d-ETH-LAD.
However I did not do any conformational distribution, all I did was draw
out the D-siomer in a 2D sketch, and converted it into a 3D .pdb file.
When I uploaded the .pdb file into AutoDock Tools, it worked--to the
extent that it loaded the proper 3D orientation, and it was the right
isomerization.

However, in AutoDock Tools, when i selected grid>set map ypes>choose
ligand, and selected the ETHLAD, it says it didnt work because it only
reads pdbqt files!

MarvinSketch seems to not have any option to save in .pdbqt format. So I
tried converting the pdb file into pdbqt using OpenBabel, a conversion
software. However, when I tried uploading the converted pdbqt ligand
file into AutoDock Tools (by selecting ligand>input>open), it says it
cant read it!

It seems there was a problem when converting the .pdb file to .pdbqt. Is
there an extra step i need to do in either OpenBabel or MarvinSketch? I
will read over the link you just sent me. Thank you so much~

Best regards! :)

On 3/5/2016 5:37 PM, Richard  Wood wrote:
> I am sure if you go to https://www.chemaxon.com/library/, there is something that will help you there.
>
> Richard
> ________________________________________
> From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on behalf of sandra [sandra at theindoleshop.com]
> Sent: Thursday, March 03, 2016 2:35 PM
> To: autodock at scripps.edu
> 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 scripps.edu [autodock-bounces at scripps.edu] on behalf of sandra [sandra at theindoleshop.com]
>> Sent: Wednesday, February 24, 2016 4:31 PM
>> To: autodock at scripps.edu
>> 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
>> (https://www.youtube.com/watch?v=ZiuqSzqcD7M) 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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