Dear Jason, Daniel and Amber users,
The make install and make test command ran perfectly, but strangely I'm not
able to run any command on the terminal. It gives the following message for
commands like sander, ptraj, tleap etc. I have checked $AMBERHOME is set
correctly. I wonder if some links were not properly created or what? Please
help me track the problem and let me know if more information is needed to
understand issue.
gm.linux-rfml:/usr/local/amber12> ptraj
If 'ptraj' is not a typo you can use command-not-found to lookup the
package that contains it, like this:
cnf ptraj
gm.linux-rfml:/usr/local/amber12>
==============================================================
Finished serial test suite for Amber 12 at Thu Jan 31 10:34:39 IST 2013.
make[2]: Leaving directory `/usr/local/amber12/test'
478 file comparisons passed
1 file comparisons failed
1 tests experienced errors
Test log file saved as
/usr/local/amber12/logs/test_amber_serial/2013-01-31_10-14-41.log
Test diffs file saved as
/usr/local/amber12/logs/test_amber_serial/2013-01-31_10-14-41.diff
make[1]: Leaving directory `/usr/local/amber12/test'
Summary of AmberTools serial tests:
607 file comparisons passed
3 file comparisons failed
0 tests experienced errors
Test log file saved as
/usr/local/amber12/logs/test_at_serial/2013-01-31_09-47-13.log
Test diffs file saved as
/usr/local/amber12/logs/test_at_serial/2013-01-31_09-47-13.diff
On Wed, Jan 30, 2013 at 6:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Jan 30, 2013 at 8:11 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Daniel and Jason,
> > I realized my mistake of not recognizing the correct patches.
> > After I have downloaded the correct patches, it seems that things have
> > worked fine. As suggested on the site I have run the command
> > (./patch_amber.py) twice. At present I'm running the "make install"
> > command.
> > Regarding the proxy setting I did not really understand the discussion as
> > I'm not a networking expert.
> > But I'm happy that the other way round seems to have worked. (With amber
> > there is something new to learn everyday).
> > Thanks all for your time and suggestions.
> >
> > ---------
> > linux-rfml:/usr/local/amber12 # ./patch_amber.py --update-tree
> > Determining patches to download for AmberTools12
> > AmberTools12 is up to date. Nothing to download
> >
>
> Don't forget to add the AmberTools bug fixes to that repository. I'm
> skeptical they have all been added already.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 30 2013 - 22:00:03 PST
