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Bug #1235

peptide dihedral angle definitions violate IUPAC

Added by Mark Abraham over 6 years ago. Updated over 4 years ago.

Status:
New
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
probably all versions since prehistoric times
Affected version:
Difficulty:
uncategorized
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Description

(and related code probably does who knows what other nasty stuff!)

Standard IUPAC definititions of phi/psi/omega angles (http://www.chem.qmul.ac.uk/iupac/misc/ppep3.html#320) are only vaguely followed by the code for g_chi. Perhaps other code like g_rama or g_angle has related problems.

These definitions should follow IUPAC and probably be implemented via selections in 5.0. At the very least, the lookups via atom names should be consolidated in one place. Numerous bugs have already been revealed by the CHARMM convention of naming hydrogen bonded to nitrogen as "NH", which was not anticipated by the original developers of various GROMACS tools, who hard-coded other strings in multiple places.


Related issues

Related to GROMACS - Bug #953: fix for g_chi omega angle calculationClosed06/02/2012
Related to GROMACS - Bug #1481: g_chi output file chi.log reports atomic definitions for phi and psi that do not correspond to the angles output in the .xvg filesNew04/11/2014

History

#1 Updated by Rossen Apostolov over 5 years ago

  • Related to Bug #1481: g_chi output file chi.log reports atomic definitions for phi and psi that do not correspond to the angles output in the .xvg files added

#2 Updated by Erik Lindahl over 5 years ago

  • Target version changed from 5.0 to 5.x

#3 Updated by Erik Lindahl over 4 years ago

  • Target version changed from 5.x to future

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