Dear Daniel,
Ops, I guess $AMBERHOME/bin was not in path. I have made this change and
its working.
Sorry for the trouble.
On Thu, Jan 31, 2013 at 11:35 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>wrote:
> Dear Daniel,
> As I said $AMBERHOME is in my path.
>
> gm.linux-rfml:/usr/local/amber12> echo $PATH
>
> /home/vaibhav/bin/oniomtool:/home/vaibhav/software/vmd_files_exceutables/start_scripts/:/home/vaibhav/bin/oniomtool:/home/vaibhav/software/vmd_files_exceutables/start_scripts/:/home/gm/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/jvm/jre/bin:/usr/local/amber12/exe:/usr/local/amber12/exe
> gm.linux-rfml:/usr/local/amber12>
>
> gm.linux-rfml:~> cd $AMBERHOME
> gm.linux-rfml:/usr/local/amber12>
>
>
>
> On Thu, Jan 31, 2013 at 11:31 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
>
>> 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
>>
>
>
>
> --
> 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
>
--
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
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Received on Wed Jan 30 2013 - 22:30:05 PST
