Bug #800

pdb2gmx creates additional incorrect cmap entries

Added by Roland Schulz over 8 years ago. Updated almost 8 years ago.

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


If some non amino acid residue(s) follow(s) the last amino acid, an additional cmap entry is generated. It is centered on the last amino acid and connects to the first N in the non-amino acid residue. The additional residues have to be bonded to the protein (like glycosylation) and thus be in the same segment for the error to occur.

The logic which creates the cmap entries (gen_cmap in pdb2top.c) should either take into account the termini detection (it works correctly in this case) or check that the previous or next residue participating in the cmap entry are protein residues (using residuetypes.dat). Not sure what is the best strategy.

Related issues

Related to GROMACS - Bug #886: pdb2gmx -cmap needs some mention in manual section 5.6Closed02/21/2012

Associated revisions

Revision 4e4d743f (diff)
Added by Mark Abraham almost 8 years ago

Fix pdb2gmx -cmap in corner cases

CMAP torsions are only generated when the atoms are from the same chain
(pdb2gmx -merge allows multiple chains to be present in the
moleculetype), and their residues are in residuetypes.dat as

Fixes #800, #885

Change-Id: Idc4f9a867beedc0be6a4c153606c0731eec86f5f


#1 Updated by Rossen Apostolov over 8 years ago

  • Assignee set to Pär Bjelkmar

#2 Updated by Roland Schulz about 8 years ago

  • Target version set to 4.5.5

#3 Updated by Rossen Apostolov about 8 years ago

  • Target version changed from 4.5.5 to 4.5.6

#4 Updated by Mark Abraham almost 8 years ago

I don't have a test case, but I believe fixes this.

#5 Updated by Roland Schulz almost 8 years ago

  • Status changed from New to Closed

#6 Updated by Mark Abraham almost 8 years ago

  • Category set to preprocessing (pdb2gmx,grompp)
  • Assignee changed from Pär Bjelkmar to Mark Abraham

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