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

From: onetwo <>
Date: 2 Jul 2013 07:38:02 -0000

Dear Jason,

Thanks a lot for the help.


On Mon, 01 Jul 2013 20:47:19 +0530 wrote

>On Mon, Jul 1, 2013 at 9:11 AM, Bill Miller III wrote:

> You shouldn't be trying to execute the scripts in the source directory. Do

> and 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 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 calculations.


Minor correction for clarity here -- the latest version is AmberTools 13

(and that is available for free download at

The installation procedure for AmberTools 13 is drastically simpler than

that for AmberTools 1.5.

Good luck,


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
AMBER mailing list
Received on Tue Jul 02 2013 - 01:00:02 PDT
Custom Search