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Bug #2225

gmx trjcat -o pdb doesn't work

Added by Mark Abraham over 2 years ago. Updated almost 2 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
analysis tools
Target version:
-
Affected version - extra info:
all versions, probably
Affected version:
Difficulty:
uncategorized
Close

Description

On gmx-users, someone reported trying gmx trjcat -f a.pdb b.pdb -o combined.pdb and after preliminary setup, being informed that there were no atom names to write in the file.

Either the atom names present in the input frames should be retained (not possible in the current data structures), or something like -s sample.pdb supported as a source of such data for each frame written out.

Presumably that means gmx trjcat -f a.xtc b.xtc -o combined.pdb is also broken, but that is something of a blessing


Related issues

Related to GROMACS - Task #2115: trjconv does too many things, and combinations of them work poorlyNew

Associated revisions

Revision c232242c (diff)
Added by Erik Lindahl almost 2 years ago

Disallow ascii formats for gmx trjcat

Since trjcat (deliberately) does not use any TPR file,
the tool can't handle trajectory formats such as GRO
or PDB where atom/residue names are needed.

Fixes #2225.

Change-Id: I55cbfd5f8a3909c1f76e63fa402f0c3243a6f7c7

History

#1 Updated by Mark Abraham over 2 years ago

  • Related to Task #2115: trjconv does too many things, and combinations of them work poorly added

#2 Updated by Gerrit Code Review Bot almost 2 years ago

Gerrit received a related patchset '1' for Issue #2225.
Uploader: Erik Lindahl ()
Change-Id: gromacs~release-2018~I55cbfd5f8a3909c1f76e63fa402f0c3243a6f7c7
Gerrit URL: https://gerrit.gromacs.org/7330

#3 Updated by Erik Lindahl almost 2 years ago

  • Status changed from New to Fix uploaded

Fixed by only allowing TRR, XTC, TNG.

#4 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Fix uploaded to Resolved

#5 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

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