APL calculation bug

[davidRFB]

Hi !

I am using FATSLiM to calculate the APL of a system with 15 % of Ligands into a membrane of DMPG.

but this problem came out !

fatslim apl --t ../traj_comp.xtc --conf ../step7_0ns.gro --index fat_ndx.ndx --plot-apl PLOT_APL FATSLiM - Fast Analysis Toolbox for Simulations of Lipid Membranes version 0.2.2 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: 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 "/home/david/anaconda3/lib/python3.7/site-packages/fatslimlib/init.py", line 132, in main exit_code = _command_registry.run(argv) File "/home/david/anaconda3/lib/python3.7/site-packages/fatslimlib/command.py", line 211, in run cmd_obj.run_with_args(command_args) File "/home/david/anaconda3/lib/python3.7/site-packages/fatslimlib/command.py", line 405, in run_with_args self._run() File "/home/david/anaconda3/lib/python3.7/site-packages/fatslimlib/command.py", line 477, in _run nframes = super(AnalyticalCommand, self)._run() File "/home/david/anaconda3/lib/python3.7/site-packages/fatslimlib/command.py", line 360, in _run output = self.run() File "/home/david/anaconda3/lib/python3.7/site-packages/fatslimlib/command.py", line 528, in run self.initialize_trajetory(traj) File "/home/david/anaconda3/lib/python3.7/site-packages/fatslimlib/command.py", line 489, in initialize_trajetory interacting_group=self.namespace.interacting_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'

Sorry, I made a boo boo...

Thanks for your time and consideration!

Best Regards David

[sizeineb]

Hi David,

I am having the same error message when using FATSLiM to calculate membrane thickness. Did you manage to fix the problem?

Best, Zeineb

[sizeineb]

I found the problem. The parameter --hg-group should be specified if the headgroups in the index file were not renamed. We have to specify the name of the group to use in the index file with the option --hg-group.