AutoDock-Vina

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bug in prepare_receptor4.py: -e flag does not have any effect

2

Yes, I know, `prepare_receptor4.py` is not part of vina... If there is a better place to report this issue please let me know - so far I was not able...

rczerminski-valo

Flexible docking tutorial : no HD map file after autogrid4

4

Dear all, I am trying a flexible docking tutorial. I am facing a problem with the generation of the map files. I am using a file `1fpu_receptorH.pdb` from the data...

mandar5335

Stack overflow during prepare_flexreceptor

5

Dear all, thank you for developing great tools. During preparation of a protein for flexible docking I am getting a `MemoryError: Stack overflow` during the last code segment when `AD4FlexibleReceptorPreparation`...

missuse

Exhaustibility, box size, and consistency

2

In an off-the-cuff remark, the official documentation advises setting exhaustibility at `32`, rather than the default `8`, for a `20*20*20` box but there's nothing more on these aspects. Certain bioinformaticists...

DarthSaddest

python support for Mac m1

1

Is there any plan to add python support for autodock-vina for the M1 Macs? This would be super useful!

hnisonoff

Conformations and Docking

4

A few questions: 1. Is there any significant downside to inputting a ligand as a 2D .pdbqt file rather than its 3d equivalent? 2. Assuming the answer to (1) is...

DarthSaddest

using --batch option to dock several hundred molecules

1

I am dealing with several hundred ligands in pdbqt format stored in a directory. Could you please give me a clue on how can I do the docking in the...

Sinsilcobio

Result with seed is not reproducible using the python version vina, and also differ from the one shown in the tutorial document

1

I was using the input files provided in the repository (basic docking), and got the following result: Scoring function : vina Rigid receptor: receptors/1iep_receptor.pdbqt Ligand: ligands/1iep_ligand.pdbqt Center: X 15.19 Y...

chiwwong

Installing Autodock Vina for use in Chimera?

5

I've downloaded the mac os file "vina_1.2.3_mac_x86_64" and put it into a folder on my mac. I've set the Autodock Vina to run as a local file and pointed Chimera...

Knots-hocks

Please make a batch submission example.

3

Please make a batch submission example.

jpmfc6