Yes, I messed up the syntax, so I tried it again and it worked! Thanks
On Thu, Jul 12, 2018 at 12:37 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
> >
> _______________________________________________
> AMBER mailing list
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>
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Received on Thu Jul 12 2018 - 14:00:02 PDT
