Ligand Parameter Generator Based on
Jorgensen group's OPLS-AA/CM1A(-LBCC) FF
Created on Mon Feb 15 15:40:05 2016
@author: Leela S. Dodda leela.dodda@yale.edu
@author: William L. Jorgensen Lab
Description of the issue
We think that the BOSS binary is interpreting the environment variable $BOSSdir as a string with a limited length (possibly ~80 characters) and that this leads to crashes when the absolute path to the BOSS program is deep. Specifically, what we have noticed is that when BOSS is installed in a location with a long absolute path, the BOSS call fails with an error message about “ERROR ENCOUNTERED WHILE OPENING A FILE IN GETUNITS” when $BOSSdir is set as an absolute path, but we can get the call to succeed when $BOSSdir is set as a relative (and therefore in this case shorter) path.
Issue Information
BOSS version 4.9 (unpacked from boss0615.tar.gz)
$ LigParGen -h usage: LigParGen [-h] [-r RESNAME] [-s SMILES] [-m MOL] [-p PDB] [-o {0,1,2,3}] [-c {0,-1,1,-2,2}] [-l]
Description of the issue
We think that the BOSS binary is interpreting the environment variable $BOSSdir as a string with a limited length (possibly ~80 characters) and that this leads to crashes when the absolute path to the BOSS program is deep. Specifically, what we have noticed is that when BOSS is installed in a location with a long absolute path, the BOSS call fails with an error message about “ERROR ENCOUNTERED WHILE OPENING A FILE IN GETUNITS” when $BOSSdir is set as an absolute path, but we can get the call to succeed when $BOSSdir is set as a relative (and therefore in this case shorter) path.