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Feature #2428

Add way of selecting interactive arguments of pdb2gmx by string rather than an index

Added by Viveca Lindahl over 1 year ago.

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

Specifying choices for e.g. termini and histidine protonation ("-ter" and "-his") in calls to pdb2gmx is currently pretty inconvenient to do from within a script. Even if one knows beforehand exactly what choices should be made, the best way I've found to do the selection is to perform a dummy pdb2gmx with dummy selections run in order to parse out the right list indices (then run pdb2gmx again providing that string as input). It would be cleaner to be able to pass the actual strings to be selected, in the same way as for in several other gmx tools.

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