Robert,

It is now working perfectly. Thank you very much for your assistance!

Max

Hi Robert, Thanks a lot for getting back to me! This is the command line option I used: ConvertDataToHDF.py -s cpn-nowat.pdb -i ./DCD -S file Here are the exceptions: -------------------------------------------------------------------------------- Looking for file style data in ./DCD WARNING: Sortin...

Hi Robert, Thanks for your reply! I prepended my epd dirctory in my $PATH and then it worked. However, the 2.5 version seemed not to be working properly in terms of the ConverDataToHDF.py script, it always gave me error on “Index out of range", which I could not really understand. I took a step back...

Dear all, I am trying to update the msmbuilder on my machine to 2.5 version. However, I got this error when I try to use any of the modules after installation: " $home/Max/Programs/MSMBuilder2.0/bin/ConvertDataToHDF.py -h Traceback (most recent call last): File "/home/Max/Programs/MSMBuilder2.0/bin/...

Dear All, Upon reading the first paper of MSMBuilder, "Using generalized ensemble simulations and Markov state models to idetify conformational states", I found it referred us to the upcoming paper regarding the determining of the transition rates in the last sentence of the "Concluding Remarks" sec...

This works great, saves me a whole lot of time! Thanks again, Josh!

Hi Alex, Hi Josh,

Thank you so much for your reply! I spent a whole day before I posted it. Seems like I should have done it earlier It gives me a heads up that I probably need to look into the scripts more carefully. Thanks again!

Cheers,

Max

Hi All, On webpage http://wiki.simtk.org/msmbuilder/User_Contributions, we found that " The DCD reader is already included in the latest MSMBuilder release s". However, even when I tried " ConvertDataToHDF.py -s ./dipeptie.pdb -I ~/msmbuilder2.0/Tutorial/DCD" to read the DCD format instead the XTC f...