AutoDock-Vina

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Hello, Is it possible to optimize the ligand using explicit receptor atoms with the "local_only" command, similar to what happens at the end of global_search? https://github.com/ccsb-scripps/AutoDock-Vina/blob/develop/src/lib/vina.cpp#L825 seems to only perform...

clockhart

I realized that the example input data for the receptor have the suffix "H", I believe that means the hydrogen atoms have been added. However, I found a hard time...

chiwwong

ubuntu 20.04 crashes

4

I downloaded the 1.2.2 release binary to Ubuntu 20.04, and it crashed very quickly after I launched the program with the message "killed", while I set verbosity=2, I still didn't...

sherwoodyao

An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69).

3

Scoring function : vina Rigid receptor: liep.pdbqt Ligand: ligand.pdbqt Grid center: X 15.19 Y 53.903 Z 16.917 Grid size : X 20 Y 20 Z 20 Grid space : 0.375...

jianwen350

Release v1.2.5

13

What is file "vina_1.2.5_mac_x86_64" as it does not appear to run? Have an older bin file "vina" 1_1_2 from scripps and that runs. Thanks Colin

alchymy

Autogrid4 Atom Type Error with Large Ligand Database

6

While attempting virtual screening with the Enamine DDS-10 ligand database (~50k compounds), I encountered an error during the grid map file generation using autogrid4. The error message is the following...

R-Stefano

Request for support for python 3.10 and 3.11

3

Requesting the devs to add support for python 3.10 and 3.11 as python’s latest release is python 3.12 and most other libraries have moved on python 3.10 and 3.11

shreyasvinaya

Details on scoring function terms

3

Hi, thank you for this great resource! :smile: I would like to know a bit more about how the scores are calculated and what the individual terms mean - do...

AnjaConev

Modelling of whole proteins is problematically slow. This change allows a fairly old laptop to calculate the maps for GPCRs in seconds to minutes. It would hang for 10s of...

jacktday

Flexible docking of Autodock using vina

7

I want to run flexible docking using vina but ad4 as a scoring function. I have prepared by receptor using prepare_receptor.py and ligand using prepare_ligand4.py. The command I am using...

Kapalisuri