Comments (4)
Problem comes from pyparsing
version 3.1.2, a dependency by ProDy library which is a dependency for LightDock (sorry, no control over it until ProDy nor pyparsing teams fix it). In the meantime, a workaround consists in downgrading the version to 3.1.1. Just type: pip install pyparsing==3.1.1
Please, could you confirm this solves the issue?
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works know thank you so much
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Please @tonyageall , could you specify which example and version of LightDock did you install (I assume it's the last, but just to double check). If you could also share the exact prompt it would be great.
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release Release 0.9.4 and I was trying to walk through your examples here https://lightdock.org/tutorials/0.9.3/simple_docking fails on lightdock3_setup.py 2UUY_rec.pdb 2UUY_lig.pdb --noxt --noh --now -anm
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Related Issues (20)
- Ligands are not placed in designated swarm centers HOT 6
- Performance for protein-DNA docking HOT 1
- Use MPI for simulation HOT 3
- Much larger number of swarms in restraints tutorial than shown in docs HOT 4
- [lgd_cluster_bsas.py] Clustering has failed. HOT 9
- Protein-RNA docking HOT 22
- How to choose swarms? HOT 2
- public server output pdb is renumbered HOT 2
- lgd_move_anm.py script HOT 3
- Membrane vs Transmembrane HOT 1
- Where is lightdock3_setup.py script generated? HOT 4
- Defining steps to run inference HOT 1
- LightDock not running with any proteins. HOT 2
- Membrane atoms not being recognised (BJ) HOT 5
- Lightdock reproducibility across different plataforms using the same seed HOT 1
- How many swarms should I simulate? HOT 1
- ValueError: max() arg is an empty sequence HOT 3
- Problem with lightdock3_setup.py HOT 1
- ERROR: Number of atoms in ProDy (5957) vs LightDock (5963)
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