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For people getting errors  #4

@guilxavi

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@guilxavi

This message is to all people that might get the following error below or messages related to parsing issues:
yaml-cpp: error at line 4, column 14: bad conversion
mv: cannot stat 'output.coor': No such file or directory
mv: cannot stat 'output.vel': No such file or directory
mv: cannot stat 'output.xsc': No such file or directory
@> 226933 atoms and 1 coordinate set(s) were parsed in 3.14s.
Traceback (most recent call last):
File "/proj/theo-storage/users/x_xavgu/SuMD-1.0.0/suMD", line 646, in
Monitor1.ANA('suMD-step{}.dcd'.format(su.stepsuMD), 'attempting')
File "/proj/theo-storage/users/x_xavgu/SuMD-1.0.0/suMD", line 148, in ANA
self.distance_dcd(fdcd, self.distance_pdb("Distance-step1.dat"))
File "/proj/theo-storage/users/x_xavgu/SuMD-1.0.0/suMD", line 117, in distance_dcd
dcd = DCDFile(fdcd)
File "/home/x_xavgu/.conda/envs/sumd24/lib/python3.10/site-packages/prody/trajectory/dcdfile.py", line 49, in init
TrajFile.init(self, filename, mode)
File "/home/x_xavgu/.conda/envs/sumd24/lib/python3.10/site-packages/prody/trajectory/trajfile.py", line 50, in init
self._file = open(filename, mode)
FileNotFoundError: [Errno 2] No such file or directory: 'suMD-step1.dcd'

I've had this error for a long long time (back in 2023 already) and couldn't figure out why, and therefore try SuMD on my system.
I finally managed to figure out that the four AMBER protocol files of the current version available on Github were responsible for these errors (input_go_AMBER_norandom.bk; input_go_AMBER_normal.bk; input_start_AMBER_norandom.bk; input_start_AMBER_normal.bk).
They are written very differently than the CHARMM files, contain headers, comments, and blank lines. On principle all good practices, except that it seems the parser doesn't know how to handle it.
Luckily, I had older files from May 2024 and with which everything works.
I'm attaching to this post my working SuMD zip folder for the community in case it could help someone else.
SuMD-main_WORKING.zip

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