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Bug #896

CHARMM atom naming in g_helix

Added by Justin Lemkul about 5 years ago. Updated about 5 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
analysis tools
Target version:
Affected version - extra info:
4.5.5
Affected version:
Difficulty:
uncategorized
Close

Description

Similar to bug #788, the naming of amide protons in the CHARMM force field (HN instead of H) causes g_helix to erroneously fail, as reported on the mailing list.

http://lists.gromacs.org/pipermail/gmx-users/2012-March/069155.html

Mark's fix for #788 works fine for g_hbond, but wouldn't it make sense to standardize nomenclature of these atoms at the .rtp level, as well?

Associated revisions

Revision b76d7b90 (diff)
Added by Mark Abraham about 5 years ago

Made g_helix sensitive to CHARMM atom naming

Peptide N-H atoms named HN in CHARMM were not recognized as backbone
atoms.

Fixes #896

Change-Id: I205b8dc5c895f20e6cde61ee2a1640fc6414b030

History

#1 Updated by Justin Lemkul about 5 years ago

  • Assignee deleted (David van der Spoel)

#2 Updated by Justin Lemkul about 5 years ago

  • Affected version - extra info set to 4.5.5

#3 Updated by Mark Abraham about 5 years ago

  • Assignee set to Mark Abraham
  • Target version set to 4.5.6

Standardizing amide H nomenclature within GROMACS would mean coordinate file incompatibility with CHARMM and CHARMM implementations, so generates about as many problems as it might solve. Fix uploaded to gerrit. I don't have a test case - testing would be welcome.

#4 Updated by Rossen Apostolov about 5 years ago

I guess we can close this one?

#5 Updated by Mark Abraham about 5 years ago

  • Status changed from New to Closed

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