Robert,
It is now working perfectly. Thank you very much for your assistance!
Max
Search found 8 matches
- Thu Jul 12, 2012 1:14 pm
- Forum: MSMBuilder
- Topic: MSMBuilder2.5 Installation
- Replies: 7
- Views: 2045
- Thu Jul 12, 2012 7:59 am
- Forum: MSMBuilder
- Topic: MSMBuilder2.5 Installation
- Replies: 7
- Views: 2045
Re: MSMBuilder2.5 Installation
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...
- Tue Jul 10, 2012 8:47 pm
- Forum: MSMBuilder
- Topic: MSMBuilder2.5 Installation
- Replies: 7
- Views: 2045
Re: MSMBuilder2.5 Installation
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...
- Sun May 27, 2012 3:04 pm
- Forum: MSMBuilder
- Topic: MSMBuilder2.5 Installation
- Replies: 7
- Views: 2045
MSMBuilder2.5 Installation
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/...
- Wed May 16, 2012 12:40 pm
- Forum: MSMBuilder
- Topic: Look for the reference paper on determining transition rate
- Replies: 0
- Views: 507
Look for the reference paper on determining transition rate
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...
- Sat May 05, 2012 6:49 pm
- Forum: MSMBuilder
- Topic: Failed in read in DCD by the latest MSMBuilder
- Replies: 5
- Views: 1427
Re: Failed in read in DCD by the latest MSMBuilder
This works great, saves me a whole lot of time! Thanks again, Josh! ![Very Happy :D](./images/smilies/icon_e_biggrin.gif)
![Very Happy :D](./images/smilies/icon_e_biggrin.gif)
- Fri May 04, 2012 7:39 pm
- Forum: MSMBuilder
- Topic: Failed in read in DCD by the latest MSMBuilder
- Replies: 5
- Views: 1427
Re: Failed in read in DCD by the latest MSMBuilder
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
Thank you so much for your reply! I spent a whole day before I posted it. Seems like I should have done it earlier
![Smile :)](./images/smilies/icon_e_smile.gif)
Cheers,
Max
- Fri May 04, 2012 1:58 pm
- Forum: MSMBuilder
- Topic: Failed in read in DCD by the latest MSMBuilder
- Replies: 5
- Views: 1427
Failed in read in DCD by the latest MSMBuilder
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...