Project

General

Profile

Bug #800

pdb2gmx creates additional incorrect cmap entries

Added by Roland Schulz about 6 years ago. Updated over 5 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

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 5.6Closed2012-02-21

Associated revisions

Revision 4e4d743f (diff)
Added by Mark Abraham over 5 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
"Protein".

Fixes #800, #885

Change-Id: Idc4f9a867beedc0be6a4c153606c0731eec86f5f

History

#1 Updated by Rossen Apostolov about 6 years ago

  • Assignee set to Pär Bjelkmar

#2 Updated by Roland Schulz about 6 years ago

  • Target version set to 4.5.5

#3 Updated by Rossen Apostolov about 6 years ago

  • Target version changed from 4.5.5 to 4.5.6

#4 Updated by Mark Abraham over 5 years ago

I don't have a test case, but I believe https://gerrit.gromacs.org/#/c/506/ fixes this.

#5 Updated by Roland Schulz over 5 years ago

  • Status changed from New to Closed

#6 Updated by Mark Abraham over 5 years ago

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

Also available in: Atom PDF