MSMBuilder2.5 Installation

[Xiaojun Xu]

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:

"
$home/Max/Programs/MSMBuilder2.0/bin/ConvertDataToHDF.py -h
Traceback (most recent call last):
File "/home/Max/Programs/MSMBuilder2.0/bin/ConvertDataToHDF.py", line 24, in <module>
from msmbuilder import CreateMergedTrajectoriesFromFAH
ImportError: No module named msmbuilder
"
I actually used exactly same configurations of python in my profile files:
"PATH=$PATH:/home/Max/Programs/epd-7.3-1-rh5-x86_64/bin/
export PATH
PYTHONPATH=/home/Max/Programs/epd-7.3-1-rh5-x86_64/lib/python2.7/site-packages/
export PYTHONPATH
PYTHONHOME=/home/Max/Programs/epd-7.3-1-rh5-x86_64/
export PYTHONHOME
"

It was working properly for MSMBuilder2.0. Somehow, it stopped working now. I thought it might be a little bit confusing to have 2 versions together, then I deleted the MSMBuilder2.0. Then, what was even worse happened it I could not get it back to work even with reinstall the version 2. It gives me the same error each time.

I deleted and reinstall the EPD, and then install either the MSMBuilder2.0 or MSMBuilder2.5. Neither of them worked, still the same error. I am kind of stuck in here now. Any input will be greatly appreciated!

Max

[Robert McGibbon]

My guess is that you might be installing msmbuilder with a different version of python than what is being used by the scripts. When setting your path, can you put the /home/Max/Programs/epd-7.3.1-rh5-x86_64/bin before the rest of your path when resenting the path in your bash_profile, so that the EPD version of python is at the top of the path.

Are you installing using "python setup.py install"? If so, you shouldn't have to manually set your python path to point into the site-packages directory.

Can you try ls-ing the contents of your site-packages directory? Is msmbuilder in there?

[Xiaojun Xu]

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 and tried the 2.0.4 version, it worked perfectly. Do you by any chance know what the problem is?

Thanks a lot!

Max

[Robert McGibbon]

Max,

I'm glad that worked for you. Can you post the exception that you're getting from the ConvertDataToHDF.py? Which command line options are you passing? We made some improvements to the script in order to speed up the conversion, but there might be some holes in the test suite.

If you can give me the stack trace for the exception and the command line arguments, I might be able to see where the problem is.

-Robert

[Xiaojun Xu]

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: Sorting trajectory files by numerical values in their names.
Ensure that numbering is as intended.

Found 105 trajectories.

Loading data:
[]
Traceback (most recent call last):
File "/home/Max/Programs/epd-7.3-1-rh5-x86_64/bin/ConvertDataToHDF.py", line 216, in <module>
args.mingen, args.stride, rmsd_cutoff, args.parallel)
File "/home/Max/Programs/epd-7.3-1-rh5-x86_64/bin/ConvertDataToHDF.py", line 96, in run
parallel=parallel)
File "/home/Max/Programs/epd-7.3-1-rh5-x86_64/lib/python2.7/site-packages/msmbuilder/Project.py", line 384, in convert_trajectories_to_lh5
[new_traj_root], [stride], [atom_indices] ) )
File "/home/Max/Programs/epd-7.3-1-rh5-x86_64/lib/python2.7/site-packages/msmbuilder/utils.py", line 36, in uneven_zip
zipped = map(get, range(max(lengths)))
File "/home/Max/Programs/epd-7.3-1-rh5-x86_64/lib/python2.7/site-packages/msmbuilder/utils.py", line 34, in get
result[j] = args[j][lengths[j]-1]
IndexError: list index out of range

Max

[Robert McGibbon]

Max,

Sorry about this. One of the --source (-S) options is supposed to be file_dcd, which detects the DCD files, but this wasn't actually listed as a choice.

I have a patch file for msmbuilder2.5 that fixes the problem, and in next release we'll have this fixed for good so that it just autodetects what type of trajectory file you have.
SimTK won't let me attach the patchfile to this post, but here's a link to the file on dropbox. https://www.dropbox.com/s/tfx92ayum3kgi6q/dcd_bug.patch.

To apply the patch file, cd into the directory where you installed msmbuilder from, and then run

patch scripts/ConvertDataToHDF.py < dcd_bug.patch

Then, instead of using -S file, use -S file_dcd.

-Robert

[Xiaojun Xu]

Robert,

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

Max

[web design]

The information was useful