Hey everyone, I've been having trouble with pdb4amber to run. I've looked
through the forum and referring to dac's response to one person who had the
same problem, I have reinstalled amber to accept miniconda installation a
few months ago, and when I type the command "$AMBERHOME/bin/pdb4amber" the
following script comes up:
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/Users/alenahmetovic/Research/amber16/bin/pdb4amber source amber.sh
Traceback (most recent call last):
File "/Users/alenahmetovic/Research/amber16/bin/pdb4amber", line 6, in
<module>
from pdb4amber import pdb4amber
ImportError: No module named pdb4amber
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When trying to open pdb4amber by manually going into the folder and opening
by right-clicking on the program and then Open--> give permission to open,
the following text pops up:
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Alens-MacBook-Pro:~ alenahmetovic$
/Users/alenahmetovic/Research/amber16/bin/pdb4amber ; exit;
Traceback (most recent call last):
File "/Users/alenahmetovic/Research/amber16/bin/pdb4amber", line 6, in
<module>
from pdb4amber import pdb4amber
ImportError: No module named pdb4amber
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.
Deleting expired sessions...9 completed.
[Process completed]
_________________________________
This is the result when I check for updates:
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$AMBERHOME/update_amber --check-updates
Checking for available patches online. This may take a few seconds...
Available AmberTools 17 patches:
update.9 (modifies sander)
Released on May 21, 2018 (written by Vinicius Wilian D. Cruzeiro)
Description:
Adds an error message when users run REMD and the box sizes are not the
same across all replicas.
update.10 (modifies sander)
Released on July 07, 2018 (written by Vinicius Wilian D. Cruzeiro)
Description:
Corrects REMD error trap for different box sizes to account for
non-periodic systems.
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I am assuming since neither update mentions anything for pdb4amber, I have
the most current version? How would I go about solving this? I have checked
my sub-folders, and do have miniconda.
Finally, from the Amber manual: "This is a list of packages that AmberTools
will install if user chose “yes”: python2.7, numpy, scipy, cython, ipython,
notebook, matplotlib.", the only package that was NOT installed was
matplotlib. Not sure if that helps or not.
Appreciate any insight to this, thanks.
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Received on Wed Jul 11 2018 - 21:30:02 PDT
