Is $AMBERHOME/bin in your path? If not add it as per the installation
instructions in the manual.
try
echo $PATH
On Thu, Jan 31, 2013 at 2:53 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>wrote:
> 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
>
--
Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
sindhikara.gmail.com <http://www.dansindhikara.com>
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 30 2013 - 22:30:02 PST
