Hi:
Openmm-6.3.1 failed to read residues with negative numbers in my charmm psf file. It used to work fine in Openmm-6.2.0. I traced it back to a line
_resre = re.compile(r'(\d+)([a-zA-Z]*)')
in OpenMM-6.3.1-Linux/python/simtk/openmm/app/charmmpsffile.py
changing it to
OpenMM-6.3.1-Linux/python/simtk/openmm/app/charmmpsffile.py
seemed to have fixed the problem. Any particular reason to exclude negative residues?
Thanks!
bug for negative residue numbers in charmmpsffile?
- Henry van den Bedem
- Posts: 3
- Joined: Thu Jul 26, 2007 1:24 pm
- Henry van den Bedem
- Posts: 3
- Joined: Thu Jul 26, 2007 1:24 pm
Re: bug for negative residue numbers in charmmpsffile?
Sorry, should have read
changing it to
_resre = re.compile(r'(-?\d+)([a-zA-Z]*)')
Thanks.
changing it to
_resre = re.compile(r'(-?\d+)([a-zA-Z]*)')
Thanks.
- Jason Swails
- Posts: 47
- Joined: Mon Jan 07, 2013 5:11 pm
Re: bug for negative residue numbers in charmmpsffile?
Nope. Didn't realize PSF files used them when I wrote the parser (I use CHARMM minimally myself). I'll fix it. Thanks for the report and the fix!vdbedem wrote: Any particular reason to exclude negative residues?