Toggle navigation
Projects
People
Projects
Project categories
Biological applications
Cardiovascular system
Cell
Myosin
Neuromuscular system
Protein
RNA
Tissue
Biocomputational focus
Experimental analysis
Image processing
Network modeling and analysis
Physics-based simulation
Statistical analysis
Visualization
Communities
OpenSim
Shoulder Modeling
SimVascular
IMAG/MSM Consortium
IMAG-MSM Public Dissemination...
Biomechanics of Movement
All Communities
About Communities
Request Community
See all projects
Create a new project
About
What is SimTK?
Features
FAQ
Contact
Sign Up
Log In
OpenMM Zephyr
Share
Follow 
Project
Follow publicly
Follow privately
Unfollow
See followers (2)
List
Map
More info
352
About
Project summary
Project statistics
Downloads Summary
Project Activity Plots
Geography of Use
Forum Statistics
Publications
Team members
Downloads
Forums
Wiki
Source Code
Summary
Browse source code
Issues
View trackers
Bugs
Bugs tracker
Submit new
Follow
Features
Features tracker
Submit new
Follow
Suggested Ideas
Suggested Ideas tracker
Submit new
Follow
News
About
Project summary
Project statistics
Downloads Summary
Project Activity Plots
Geography of Use
Forum Statistics
Publications
Team members
Downloads
Forums
Wiki
Source Code
Summary
Browse source code
Issues
View trackers
Bugs
Bugs tracker
Submit new
Follow
Features
Features tracker
Submit new
Follow
Suggested Ideas
Suggested Ideas tracker
Submit new
Follow
News
Trackers
Date:
2009-12-02 00:21
Priority:
3
State:
Open
Submitted by:
Jeanette Schmidt (
jeanette
)
Assigned to:
Christopher Bruns (cmbruns)
Summary:
Weird bug when new directory gets created based on molecule name
Detailed description
I ran into this strange bug on windows which should happen *very rarely* but was time consuming because I did not understand what was going on. My pdb file (don't ask why) had a"space" at the end of file name before the .pdb extension. Zephyr created a directory "without the space" - which may have gotten stripped off when the directory was created but attempted to read from the directory with the space as in "villin /villin _processed.pdb" -- that resulted in a fatal error. I did not try this on mac. Remedy is probably to strip spaces from directory name. Incidentally after Zephyr encounters such a fatal error the "cancel button" is not available -- must quit Zephyr and restart it, to do a new run. This is kind of a freak error -- so not sure what priority to put this at
I ran into this strange bug on windows which should happen *very rarely* but was time consuming because I did not understand what was going on.
My pdb file (don't ask why) had a"space" at the end of file name before the .pdb extension.
Zephyr created a directory "without the space" - which may have gotten stripped off when the directory was created but attempted to read from the directory with the space as in "villin /villin _processed.pdb" -- that resulted in a fatal error.
I did not try this on mac.
Remedy is probably to strip spaces from directory name.
Incidentally after Zephyr encounters such a fatal error the "cancel button" is not available -- must quit Zephyr and restart it, to do a new run.
This is kind of a freak error -- so not sure what priority to put this at
Comments
Attachments
Changes
Add A Comment:
No Comments Have Been Posted
No Changes Have Been Made to This Item
#FDF8E1 @light_yellow
#F75236 @red
#F5B563 @orange
#81A5D4 @light_blue
#5E96E1 @dark_blue
#505050 @dark_grey
#000000 @black
#A7A7A7 @light_grey
Feedback