Running Autodock Vina with batch Ligand occur error basic_string::_M_replace_aux

[oceanzyl]

I running AutoDock Vina version 1.2.5 on Mgltool 1.5.7 with batch Ligand parameter. And I have met the result the following error occurred basic_string::_M_replace_aux Anyone have an idea about the solution. I would be appreciate it

Scoring function : vina
Rigid receptor: p2k1_B99990009.pdbqt
Grid center: X 0 Y 99.366 Z 16.226
Grid size  : X 18.75 Y 18.75 Z 18.75
Grid space : 0.375
Exhaustiveness: 8
CPU: 0
Verbosity: 1

Computing Vina grid ... done.


An error occurred: basic_string::_M_replace_aux.

[rwxayheee]

Hi @oceanzyl Could you explain a little more information about how you run Vina 1.2.5 on MGLTools? An error occurred: basic_string::_M_replace_aux. This looks like a C++ error. But it's not entirely clear where it occurred. Could you provide input files so others can reproduce it?

[oceanzyl]

In Mgltool, I import the vina's path (download [vina_1.2.5_linux_x86_64] from (https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.5/vina_1.2.5_linux_x86_64) and config.txt file as below:

receptor = p2k1_B99990009.pdbqt
batch = [ directory of folder contains ligands as pdbqt file]   #In my case: /home/oceanzyl1807/Dorn1_prediction/Modeller/P2K1_v4_1000/article_template/docking/AutoDock/p2k1-179/ATP/p2k1-179009-ligand-torsion/ATP_torsion/ATP_pubchem(1-10)
center_x = 10.717
center_y = 99.366
center_z = 16.226
size_x = 18.75
size_y = 18.75
size_z = 18.75
num_modes= 20
dir = [ directory for the docking result files]
# In my case /home/oceanzyl1807/Dorn1_prediction/Modeller/P2K1_v4_1000/article_template/docking/AutoDock/p2k1-179/ATP/p2k1-179009-ligand-torsion/ATP_torsion/ATP-gb3-20result-batch(1-10)_out

It was running normally when i docked one ligand.

[rwxayheee]

Hi @oceanzyl! I have a walkaround (may not be the best solution) for you. Below is a sample config file for batch docking:

receptor = 1iep_receptor.pdbqt
batch = batch_ligands/ligand_1.pdbqt
batch = batch_ligands/ligand_2.pdbqt
batch = batch_ligands/ligand_3.pdbqt
center_x = 15.190
center_y = 53.903
center_z = 16.917
size_x = 20.0
size_y = 20.0
size_z = 20.0
dir = batch_output

This worked for me with the command-line vina. I was also able to run it through PMV (MGLTools 1.5.7)

ps. i can reproduce the same error if I let "batch" be the directory name of ligand files. Specification of input directory like this may not be currently supported

batch = [ directory of folder contains ligands as pdbqt file]