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Bug #388

Acetyl angle parameters missing from .rtp files

Added by Justin Lemkul over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

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.

History

#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.

#2 Updated by David van der Spoel over 9 years ago

Added explicit angle in ACE declaration in gromacs 43a1, 43a2, 45a3 aminoacid.rtp files, in order to fix bug 388.

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