MantisBT - Rosetta
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IDProjectCategoryView StatusDate SubmittedLast Update
0000108Rosetta[All Projects] Input Handlingpublic2012-09-19 13:312012-09-19 13:47
Reporterrmoretti 
Assigned To 
PrioritynormalSeverityminorReproducibilityalways
StatusnewResolutionopen 
PlatformAll platformsOSAnyOS VersionAny
Product VersionTrunk 
Fixed in Version 
Application(s) Affectedmolfile_to_params.py; backrub
Command Line Usedany with backrub
Developer OptionsFeature Request
Fixed in SVN Version
Summary0000108: molfile_to_params.py does not play well with backrub
DescriptionWhen setting up a ligand/non-canonical amino acid with molfile_to_params.py, it cheats and give X to all atoms for the molecular mechanics atom types. While normally this isn't a problem, it can cause issues with things like backrub, which expect parameterizable MM atom types and crash if given X's (cf. http://www.rosettacommons.org/content/backrub-params-files [^] )

It might be nice to have molfile_to_params.py give semi-reasonable MM atom types to ligand atoms. (If more precise atom typing is desired, people can always post edit the params file.)
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Issue History
Date ModifiedUsernameFieldChange
2012-09-19 13:31rmorettiNew Issue
2012-09-19 13:47smlewisNote Added: 0000105

Notes
(0000105)
smlewis   
2012-09-19 13:47   
Sam changed molfile_to_params in 50204 to put VIRT instead of X, bug 0000004

I agree with you in a perfect world that molfile_to_params should assign mm_types instead of dodging the issue, but I think Sam's patch is the best that's likely available. Close as duplicate?