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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
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An input file contains a line longer than 4095 characters #26

Closed kexul closed 3 years ago

kexul commented 3 years ago

Hi, my PDBId is 6h3k, I used protocaller to prepare my system. In minimization, gmx grompp raised an error: Fatal error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: ' 4134 4135 '

Here is my complex_final.top generated by protocaller, in line 9461, there are many @ characters.

complex_final.zip

kexul commented 3 years ago

But the complex.top is fine in the line contain 4134 4135. image

complex.zip

msuruzhon commented 3 years ago

Is this error reproducible? I have had similar looking errors in a completely different setting (not related to ProtoCaller) when there is a problem with file I/O, and that results in these null characters ^@ being written out for some reason. Also, does the file work if you manually remove the null characters in vim?

kexul commented 3 years ago

It's not always reproducible, this is the first time I encountered it. I have not encountered it before, even with the same protein. That's a good idea, I'll try remove it manually.

kexul commented 3 years ago

It worked, thanks.