Bug #619

Improper handling of force field directories by pdb2gmx

Added by J. Nathan over 9 years ago. Updated over 9 years ago.

preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:


This bug is in version 4.5.3. When I copy the complete, intact oplsaa.ff directory from share/top to a working directory, and then modify charges in the working directory copy of oplsaa.ff/aminoacids.rtp, pdb2gmx generates a topology file based on the modified copy of oplsaa.ff/aminoacids.rtp no matter if I pick force field 1 (oplsaa.ff from my working directory) from the interactive menu or force field 15 (oplsaa.ff from the share/top directory). I have confirmed this behavior several times, and have also noted that if I delete the oplsaa.ff/aminoacids.rtp file from the working directory pdb2gmx crashes and says it can't find a .rtp file, and this happens even if I pick the share/top/oplsaa.ff force field.

It seems that pdb2gmx is giving precedence to the working directory copy of the force field and essentially ignoring the choice the user makes in the interactive menu. I did discover that if I rename the working directory copy of the force field directory to something different (oplsaa2.ff for instance) then pdb2gmx will let me select between the 2 copies of the force field and will yield the appropriate topology file (correct charges based on which aminoacids.rtp file was used).

Perhaps this isn't really a bug so much as a warning that one must name the force field directory in a working directory something different than the share/top version of the directory in order to be able to choose between them correctly.

Associated revisions

Revision 565cf5c4 (diff)
Added by Berk Hess over 9 years ago

add pdb2gmx check for multiple .ff directories

pdb2gmx will currently always read from the first .ff directory
in the library directory search list. Therefore selecting a second
force field with the same directory name would still lead to reading
the files in the first directory. A verbose fatal error now occurs
when not choosing the first of multiple entries.
This fixes #619


#1 Updated by Berk Hess over 9 years ago

  • Category changed from mdrun to preprocessing (pdb2gmx,grompp)
  • Status changed from New to Closed
  • Assignee changed from Erik Lindahl to Berk Hess
  • Target version changed from 4.5.1 to 4.5.4

This is a nasty bug, because it might lead to using unwanted parameters if you don't read
your output carefully. I have now added a fatal error in case you try to select a second
entry in the list with the same ff directory name:
gmx_fatal(FARGS,"Can only select the first of multiple force field entries with directory name '%s%s' in the list. If you want to use the next entry, run pdb2gmx in a different directory or rename or move the force field directory present in the current working directory.",


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