Acetyl angle parameters missing from .rtp files
For the Gromos96 force fields, where [angles] are explicitly defined in the .rtp file, a necessary angle is missing. When running an N-acetylated protein through pdb2gmx, an angle corresponding to CA-C-O is written to the topology, but it is missing parameters, causing grompp to fail ("No default G96Angle types"). One can manually add the required "ga_30" to the topology to fix the problem, but it would probably be preferable if pdb2gmx does this instead of writing a non-functional topology.
To fix this, the ffG*.rtp files should be be updated to include:
CA C O ga_30
in the [angles] directive of the [ACE] entry.
#1 Updated by Justin Lemkul over 9 years ago
I just realized that this bug was already fixed. I was on a machine with version 4.0.5, which had this problem, and thinking that I was on 4.0.7, I reported the issue. My mistake; I suppose this bug can be closed now since it no longer is a problem. Sorry for the false alarm.