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
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Received on Mon Jul 01 2013 - 05:00:03 PDT
