have you tried to "source amber.sh" yet?
Hai
On Thu, Jul 12, 2018 at 12:27 AM, Alen Ahmetovic <alen2.mail.usf.edu> wrote:
> 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 "$AMBERHOME/bin/pdb4amber" the
> following script comes up:
> __________________________________
>
> /Users/alenahmetovic/Research/amber16/bin/pdb4amber source amber.sh
>
> Traceback (most recent call last):
>
> File "/Users/alenahmetovic/Research/amber16/bin/pdb4amber", line 6, in
> <module>
>
> from pdb4amber import pdb4amber
>
> ImportError: No module named pdb4amber
> __________________________________
>
> When trying to open pdb4amber by manually going into the folder and opening
> by right-clicking on the program and then Open--> give permission to open,
> the following text pops up:
> _________________________________
>
> Alens-MacBook-Pro:~ alenahmetovic$
> /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:
>
> _______________________________
>
> $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.
> _______________________________
>
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 11 2018 - 22:00:03 PDT
