Comments (3)
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]
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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?
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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.
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Related Issues (20)
- Flexible docking tutorial : no HD map file after autogrid4 HOT 1
- Differences between `*_rigid.pdbqt` and `*.pdbqt` files of receptors HOT 2
- Issue : An internal error occurred in ../../../src/lib/tree.h(101) HOT 3
- Problem in generation of some map files during flexible autodock docking. HOT 3
- Error on running prepare_flexreceptor.py for flexible docking HOT 8
- Charged ligands and receptors HOT 2
- FLexible Autodock HOT 1
- Method to capture receptor structure state after flexible docking HOT 7
- Virtual screening using Python bindings HOT 22
- Autodock Vina Scoring Functions HOT 3
- How to perform docking of drugs that contain metal ions?
- REMARK VINA RESULT not in PDBQT output of `--local_only` or `--score_only` type of calculations
- Zn docking-Chelation issue HOT 9
- An internal error occurred in ../../../src/lib/tree.h(101) HOT 3
- Discrepancy Between Multi-Ligand Docking Score and Summed Individual Scores in AutoVina HOT 6
- Multiple-ligand docking pose PDBQT cannot be (re)scored HOT 1
- What kind of file is the Linux download? HOT 2
- ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects HOT 13
- `!pip install vina` failed in Google Colab, with a Linux Python 3 Google Compute Engine backend
- ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects - MacOSx HOT 1
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