Dear Bill,
Thanks a lot for the reply. Now, I m trying to run MMPBSA from $AMBERHOME/bin/.
it is working now.
Thanks a lot for the help.
On Mon, 01 Jul 2013 18:43:08 +0530 wrote
>You shouldn't be trying to execute the scripts in the source directory. Do
MMPBSA.py and MMPBSA.py.MPI exist in your $AMBERHOME/bin/ directory? If
those files do not exist in your $AMBERHOME/bin/ directory, it sounds like
they weren't ever installed properly. Also, have you tried the calculation
in serial to make sure it will work? You should always try it in serial
before attempting the calculations in parallel.
The errors you are seeing are not caused by the AmberTools version you are
using, per se, but there are upgrades and fixes to MMPBSA.py in general
that would be available only with upgrading to AmberTools 12. Also, you
would not need to re-run your MD simulations after upgrading to AmberTools
12, just the MMPBSA.py calculations.
I hope that helps.
-Bill
On Mon, Jul 1, 2013 at 7:54 AM, onetwo wrote:
> Dear Jason,
>
>
>
> Thanks a lot for the reply.
>
>
>
> We have amber11 with us and used ambertools1.5 installed with it.
>
>
>
> I am new to amber and especially its installation took me a long time.
>
>
>
> Finally it is working.
>
>
>
> But MMPBSA is not working. Like first, mmpbsa_py_energy error was coming
> and now when I was trying to give the following command:
>
> /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI and further
> inputs for the file,
>
>
>
> it gives error:
>
> bash: /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI:
> Permission denied.
>
>
>
> So, I made the file executable ( may be i m wrong in doing so). But now
> when i run the same command it is giving error:
>
> /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI: line 17:
> VERSION: command not found
>
> /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI: line 44: try::
> command not found
>
> /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI: line 45:
> except:: command not found
>
> /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI: line 46: print:
> command not found
>
> /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI: line 47: syntax
> error near unexpected token `1'
>
> /usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI: line 47: `
> quit(1)'
>
>
>
> So, I was just wondering that these errors are coming due to AmberTools
> version. Upgrading it to AmberTools12 will not give the problems.
>
> Also, I hope there will be no problem during installation/upgradation and
> later running the normal simulation jobs.
>
>
>
> I am really sorry for mailing again, Actually I subscribed to the mailing
> list for the first time and so, I thought my first mail has not been
> posted. So, I mailed again. I will take care of it next time.
>
>
>
> Thanks a lot for your help and your precious time.
>
>
>
> Regards
>
>
>
> Shivu
>
>
>
> On Mon, 01 Jul 2013 15:51:55 +0530 wrote
>
> >On Mon, Jul 1, 2013 at 2:17 AM, onetwo wrote:
>
>
>
>
>
>
>
> > Dear All,
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > I am trying to use MMPBSA script as given in tutorial.
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > While running the command /usr/local/amber11/bin/MMPBSA.MPI
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > it gives the following error:
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > Running MMPBSA.MPI on 1 processors...
>
>
>
> >
>
>
>
> > Reading command-line arguments and input files...
>
>
>
> >
>
>
>
> > Loading and checking parameter files for compatibility...
>
>
>
> >
>
>
>
> > ptraj found! Using /usr/local/amber11/bin/ptraj
>
>
>
> >
>
>
>
> > Error: mmpbsa_py_energy could not be found!
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > Please help to how to sort this problem.
>
>
>
> >
>
>
>
>
>
>
>
> Make sure AMBERHOME is set properly. If so, and there is no
>
>
>
> mmpbsa_py_energy in $AMBERHOME/bin, then you need to recompile Amber.
>
>
>
>
>
>
>
> I also strongly suggest that you install AmberTools 13 and use that
>
>
>
> version, as there have been numerous updates and improvements since
>
>
>
> AmberTools 1.4/1.5.
>
>
>
>
>
>
>
> Also, please allow at least a couple of days for someone to answer your
>
>
>
> email before reposting your question, especially when you ask over the
>
>
>
> weekend. Sending multiple emails does not always result in a faster
>
>
>
> response (for example, I would have responded this morning regardless),
>
>
>
> although people may find it irritating.
>
>
>
>
>
>
>
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-846-1633
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Received on Mon Jul 01 2013 - 07:00:03 PDT
