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openmm / pdbfixer

PDBFixer fixes problems in PDB files
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Version 1.8.1 fails to addSolvent() when boxShape kwarg is present. Also in openmm-setup #249

Closed pguillem closed 2 years ago

pguillem commented 2 years ago

Hi guys. I followed the instructions to install pdbfixer/flask/openmm via conda, later cloned openmm-setup from git.

When adding water (any box shape), an exception throws the message: TypeError: addSolvent() got an unexpected keyword argument 'boxShape'

To reproduce, run:

wget https://files.rcsb.org/download/3OUX.pdb

python
import pdbfixer
fix = pdbfixer.PDBFixer("3OUX.pdb")
fix.addSolvent(boxSize=10, padding=1, boxShape="cube")

I get the exact same error if I use openmm-setup, right after selecting the Add Water option in the GUI.

"conda list" reports that pdbfixer version is 1.8.1. Am I working with the correct version?

Thanks in advance Pedro

peastman commented 2 years ago

You're using incompatible versions. If you use the latest PDBFixer code from the repository, you also need to use the latest OpenMM code from the repository. Alternatively you can install both of them with conda, which will give you the most recent release of each one.

pguillem commented 2 years ago

Thanks Peter. Will do.

Pedro