Skip to content

Trying to run PENSA with AMBER files #75

@MauricioMartil

Description

@MauricioMartil

Hi

I have been trying to run PENSA on my trajectories from AMBER. I generated the .psf file using parmed and used my own .incprd and .prmtop but whenever I try to run extract_coordinates.py, I am getting the following error message:

Traceback (most recent call last):
File "/media/mauricio/Expansion/POT1/pensa_pot_test/work/../../AF/a/pensa/scripts/extract_coordinates.py", line 29, in
extract_coordinates(args.ref_file, args.pdb_file, args.trj_file,
File "/media/mauricio/Expansion/POT1/AF/a/pensa/pensa/preprocessing/coordinates.py", line 44, in extract_coordinates
selection.write(out_name + '.prmtop')
File "/home/mauricio/.conda/envs/pensa/lib/python3.10/site-packages/MDAnalysis/core/groups.py", line 3756, in write
raise ValueError("No writer found for format: {}".format(filename))
ValueError: No writer found for format: traj/D51N_POT1.prmtop

I would like to know how I could make PENSA work using NetCDF coordinates.

Metadata

Metadata

Assignees

Labels

enhancementNew feature or request

Type

No type

Projects

No projects

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions