jinyapan
commented
5 years ago Did u solve this problem ? Because i met the same problem like you.
Open dandalf02 opened 6 years ago
jinyapan
commented
5 years ago Did u solve this problem ? Because i met the same problem like you.
dandalf02
commented
5 years ago Unfortunately no, I gave up on it...
seb-buch
commented
5 years ago As for most of the other issues, I have been sitting on this problem for too long because I wanted to rewrite the core code to use mdanalysis. I finally have some time to spend on a proper full rewrite so hopefully this issue will be resolved when issues #7 and #9 are fixed.
jonah-lc
commented
3 years ago Hello, Any updates on this, I seem to hitting a similar error whenever I try to do anything with FATSLiM
"FATAL ERROR: b'headgroups'
Well, this was unexpected... Congrats, you probably found a bug in FATSLiM! Please report the following traceback to the devs:
Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/fatslim-0.2.2-py3.8-linux-x86_64.egg/fatslimlib/init.py", line 132, in main exit_code = _command_registry.run(argv) File "/usr/local/lib/python3.8/dist-packages/fatslim-0.2.2-py3.8-linux-x86_64.egg/fatslimlib/command.py", line 211, in run cmd_obj.run_with_args(command_args) File "/usr/local/lib/python3.8/dist-packages/fatslim-0.2.2-py3.8-linux-x86_64.egg/fatslimlib/command.py", line 405, in run_with_args self._run() File "/usr/local/lib/python3.8/dist-packages/fatslim-0.2.2-py3.8-linux-x86_64.egg/fatslimlib/command.py", line 477, in _run nframes = super(AnalyticalCommand, self)._run() File "/usr/local/lib/python3.8/dist-packages/fatslim-0.2.2-py3.8-linux-x86_64.egg/fatslimlib/command.py", line 360, in _run output = self.run() File "/usr/local/lib/python3.8/dist-packages/fatslim-0.2.2-py3.8-linux-x86_64.egg/fatslimlib/command.py", line 528, in run self.initialize_trajetory(traj) File "/usr/local/lib/python3.8/dist-packages/fatslim-0.2.2-py3.8-linux-x86_64.egg/fatslimlib/command.py", line 488, in initialize_trajetory traj.initialize(hg_group=self.namespace.hg_group, File "fatslimlib/core_base.pyx", line 1779, in fatslimlib.core_base.Trajectory.initialize File "fatslimlib/core_base.pyx", line 1296, in fatslimlib.core_base.IndexReader.getitem KeyError: b'headgroups'
"
Hello, I am having trouble using the Fatslim. Typically I try something like this: fatslim apl -c conf.gro -n index_fatslim.ndx --export-apl-raw bilayer_apl.csv
(conf.gro is a file straight from gromacs, 880 POPC molecules in water with ions index file contains only the 'headgroups' with fosphorus atoms)
and end up with this message: FATSLiM - Fast Analysis Toolbox for Simulations of Lipid Membranes version 0.2.1 Copyright (c) 2013-2016 Sébastien Buchoux
Running command: 'apl'... This may take some time, be patient! Analysis will be performed using 4 threads.
FATAL ERROR: ''
Well, this was unexpected... Congrats, you probably found a bug in FATSLiM! Please report the following traceback to the devs:
Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/fatslimlib/init.py", line 132, in main exit_code = _command_registry.run(argv) File "/usr/local/lib/python2.7/dist-packages/fatslimlib/command.py", line 211, in run cmd_obj.run_with_args(command_args) File "/usr/local/lib/python2.7/dist-packages/fatslimlib/command.py", line 405, in run_with_args self._run() File "/usr/local/lib/python2.7/dist-packages/fatslimlib/command.py", line 477, in _run nframes = super(AnalyticalCommand, self)._run() File "/usr/local/lib/python2.7/dist-packages/fatslimlib/command.py", line 360, in _run output = self.run() File "/usr/local/lib/python2.7/dist-packages/fatslimlib/command.py", line 527, in run self.verbose) File "/usr/local/lib/python2.7/dist-packages/fatslimlib/datareading.py", line 71, in load_trajectory readers = get_readers(top_file, index_file, coords_file, verbose=verbose) File "/usr/local/lib/python2.7/dist-packages/fatslimlib/datareading.py", line 66, in get_readers index_loader(index_file, verbose=verbose), \ File "fatslimlib/core_base.pyx", line 1280, in fatslimlib.core_base.IndexReader.init (fatslimlib/core_base.c:18308) self.load() File "fatslimlib/core_base.pyx", line 1288, in fatslimlib.core_base.IndexReader.load (fatslimlib/core_base.c:18521) self.fast_load() File "fatslimlib/core_datareading.pyx", line 206, in fatslimlib.core_datareading.NdxReader.fast_load (fatslimlib/core_datareading.c:4455) groups[last_group] = numpy.fromstring(groups[last_group], dtype=np.int64, sep=" ") KeyError: ''
Sorry, I made a boo boo...
Is there something obvious I am doing wrong?