Using TUPÃ v1.7.0 in LIST mode to calculate LEFs at multiple grid points (2 Å extent, 1 Å spacing) for PDB 1H55 (x.prmtop, x.pdb, single-frame, dt = 1). grid_points.txt has 125 lines of 3 space-separated floats. Errors prevent execution:
ValueError: File of coordinates could not be parsed! Expecting 3 columns (X Y Z) (utils.py, line 236).
Prior errors (fixed):
NameError: 'u' & 'ts'.
SelectionError: could not convert string to float.
NameError: 'calc_electric_field'.
LIST mode expects one point per frame, unsuitable for multi-point grids. Suggest adding GRID mode for static grids.
Steps to Reproduce:
Config: mode = LIST, file_of_coordinates = grid_points.txt, dt = 1, boxdimensions = [120.0, 120.0, 120.0, 90.0, 90.0, 90.0].
Run: TUPA.py -top x.prmtop -traj x.pdb -c config -outdir RES.
Environment:
TUPÃ: v1.7.0
Python: 3
MDAnalysis
OS: WSL/Linux
Attachments:
x.pdb
x.prmtop
config.txt
grid_points_sample.txt
config.txt
grid_points.txt
x.pdb.txt
x.prmtop.txt
Using TUPÃ v1.7.0 in LIST mode to calculate LEFs at multiple grid points (2 Å extent, 1 Å spacing) for PDB 1H55 (x.prmtop, x.pdb, single-frame, dt = 1). grid_points.txt has 125 lines of 3 space-separated floats. Errors prevent execution:
ValueError: File of coordinates could not be parsed! Expecting 3 columns (X Y Z) (utils.py, line 236).
Prior errors (fixed):
NameError: 'u' & 'ts'.
SelectionError: could not convert string to float.
NameError: 'calc_electric_field'.
LIST mode expects one point per frame, unsuitable for multi-point grids. Suggest adding GRID mode for static grids.
Steps to Reproduce:
Config: mode = LIST, file_of_coordinates = grid_points.txt, dt = 1, boxdimensions = [120.0, 120.0, 120.0, 90.0, 90.0, 90.0].
Run: TUPA.py -top x.prmtop -traj x.pdb -c config -outdir RES.
Environment:
TUPÃ: v1.7.0
Python: 3
MDAnalysis
OS: WSL/Linux
Attachments:
x.pdb
x.prmtop
config.txt
grid_points_sample.txt
config.txt
grid_points.txt
x.pdb.txt
x.prmtop.txt