openmm / pdbfixer

PDBFixer fixes problems in PDB files
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No matching distribution found for openmm>=7.1 (from pdbfixer) #244

Closed tkcaccia closed 2 years ago

tkcaccia commented 2 years ago

I am trying to install pdbfixer without success

conda install -c omnia openmm

Collecting package metadata (current_repodata.json): done Solving environment: done All requested packages already installed.

conda install -c omnia/label/beta pdbfixer

Collecting package metadata (current_repodata.json): done Solving environment: done All requested packages already installed.

python3 -m pip install openmm

Requirement already satisfied: openmm in /home/user/.local/lib/python3.8/site-packages (0.2)

python3 -m pip install pdbfixer

Requirement already satisfied: pdbfixer in /home/user/alphafold (1.8.1) Requirement already satisfied: numpy in /home/user/.local/lib/python3.8/site-packages (from pdbfixer) (1.22.3) ERROR: Could not find a version that satisfies the requirement openmm>=7.1 (from pdbfixer) (from versions: 0.1, 0.2) ERROR: No matching distribution found for openmm>=7.1 (from pdbfixer)

peastman commented 2 years ago

The omnia channel is obsolete. Install with

conda install -c conda-forge pdbfixer

tkcaccia commented 2 years ago

The installation of pdffixer seems to go well but then I get an error when I try to run Alphafold Could you please help me to understand?

python3 run_alphafold.py /media/user/Cheeta/Data/Alphafold/Input/cytC.fasta**

Traceback (most recent call last):
File "run_alphafold.py", line 39, in
from alphafold.relax import relax
File "/home/user/alphafold/alphafold/relax/relax.py", line 18, in
from alphafold.relax import amber_minimize
File "/home/user/alphafold/alphafold/relax/amber_minimize.py", line 25, in
from alphafold.relax import cleanup
File "/home/user/alphafold/alphafold/relax/cleanup.py", line 22, in
import pdbfixer
ModuleNotFoundError: No module named 'pdbfixer'