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Bug #1839

pdb2gmx: Failure to rename non-standard hydrogen atom names after generating missing hydrogens in pdb2gmx

Added by Nicholas Leioatts about 4 years ago. Updated over 3 years ago.

Status:
Accepted
Priority:
Low
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
future
Affected version - extra info:
5.0.7-dev-20150928-2caddad-unknown
Affected version:
5.0.7
Difficulty:
uncategorized
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Description

This bug is encountered when trying to use an atom renaming file (e.g. merged.arn) to rename newly-built hydrogens.
There is no rename_atoms call after the add_h function.

There is a final rename_atoms call just prior to add_h (see lines 1950 and 1987). Moving this below add_h seems to resolve the issue.
I do not know if any other errors are introduced.

(In my case this is with the charmm36 ff, but the problem should be generally applicable to non-standard names hydrogens)

reproduce.tar (3.05 MB) reproduce.tar Notes, files to reproduce error, suggested correction Nicholas Leioatts, 10/08/2015 11:51 AM

History

#1 Updated by Erik Lindahl over 3 years ago

  • Status changed from New to Accepted
  • Target version set to future

Hi Nicholas,

Unfortunately this is difficult to simply fix without possibly affecting lots of other stuff in pdb2gmx. Rather than adding a last-minute hack (which we from experience know will have other side effects), we'll finally try to get some action on the overall pdb2gmx redesign later this year, and then we'll make sure to have a flexible renaming framework in place.

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