Re: [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found

From: onetwo <>
Date: 1 Jul 2013 11:54:33 -0000

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/ and further inputs for the file,

it gives error:

bash: /usr/local/amber11/AmberTools/src/mmpbsa_py/ 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/ line 17: VERSION: command not found

/usr/local/amber11/AmberTools/src/mmpbsa_py/ line 44: try:: command not found

/usr/local/amber11/AmberTools/src/mmpbsa_py/ line 45: except:: command not found

/usr/local/amber11/AmberTools/src/mmpbsa_py/ line 46: print: command not found

/usr/local/amber11/AmberTools/src/mmpbsa_py/ line 47: syntax error near unexpected token `1'

/usr/local/amber11/AmberTools/src/mmpbsa_py/ 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.



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 M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Jul 01 2013 - 05:00:03 PDT
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