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Bug #2370

pdb2gmx does not report why chains of residues are teminated

Added by Mark Abraham 10 months ago. Updated 8 months ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
affects all versions
Affected version:
Difficulty:
uncategorized
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Description

In find_nc_ter(), the chain is terminated when a residue is found whose type does not match that of the rest of the chain. This happens frequently when users modify a residue and forget to change residuetypes.dat.

We should at least report the reason for the termination, so the user being prompted for a C terminus after the residue before the modified one can see why they are being prompted. Perhaps we should also suggest editing residuetypes.dat when this occurs.

Associated revisions

Revision 541e7d05 (diff)
Added by Erik Lindahl 9 months ago

Improve pdb2gmx for nonstandard residue types

If explicit non-blank chain identifiers are set, it
will now be a hard error if the residue types in each
chain do not match. For blank chain ID we still need
to allow detection of non-chain parts, but this case
too now provides more explicit output information.

Fixes #2370.

Change-Id: Ic70f4d91fddd80a22e91eb1a0672a15838966a75

History

#1 Updated by Gerrit Code Review Bot 10 months ago

Gerrit received a related patchset '1' for Issue #2370.
Uploader: Erik Lindahl ()
Change-Id: gromacs~release-2018~Ic70f4d91fddd80a22e91eb1a0672a15838966a75
Gerrit URL: https://gerrit.gromacs.org/7412

#2 Updated by Erik Lindahl 10 months ago

  • Status changed from New to Fix uploaded

#3 Updated by Erik Lindahl 9 months ago

  • Status changed from Fix uploaded to Resolved

#4 Updated by Erik Lindahl 8 months ago

  • Status changed from Resolved to Closed

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