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Bug #1488

pdb2gmx confused by insertion codes

Added by Erik Marklund over 5 years ago. Updated over 5 years ago.

Status:
Rejected
Priority:
Low
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

pdb2gmx includes all alternative residues specified with insertion codes. 1OVA.pdb is an expel that makes pdb2gmx do this. i suggest ignoring residues with insertion codes.

History

#1 Updated by Erik Lindahl over 5 years ago

  • Status changed from New to Rejected

Insertion code residues are not optional, but frequently used for residues that cannot be resolved (and were thus modeled), or to have the same sequence numbering between species. There are thus lots of valid cases where those residues are needed. Case in point: If you have a look at 1OVA, there would be a chain break between residue 87 and 88 of the insertion-code residues were removed.

While there might certainly be cases where you want to remove them, that is something you will have to decide manually before running pdb2gmx.

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