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Feature #2429

Add option of periodic chain topology to pdb2gmx

Added by Viveca Lindahl over 1 year ago. Updated over 1 year ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
-
Difficulty:
uncategorized
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Description

Currently pdb2gmx cannot generate a periodically connected chain topology, useful e.g. for a polymer or DNA/RNA systems. In addition to not being supported, pdb2gmx can make the "manual" topology generation difficult because it will refuse to generate topologies with missing bonds. It would at least help to have a flag allowing the user trying to manually modify the topology to generate such broken topologies (note: to my understanding this is what the -missing flag should do, but in practice this flag does not always avoid the fatal error of "dangling bonds").

History

#1 Updated by Viveca Lindahl over 1 year ago

Update: change https://gerrit.gromacs.org/#/c/7660/ now allows pdb2gmx to be more "generous", so adding -missing will avoid the fatal error for missing bonds.

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