Re: [AMBER] Fw: Re: MMPBSA problem

From: Jason Swails <>
Date: Wed, 31 Jul 2013 23:20:50 -0400

On Wed, Jul 31, 2013 at 10:01 PM, 372133720 <> wrote:

> 372133720
> From: tianchuan1015
> Date: 2013-07-31 15:39
> To: prajwal.pharm07
> Subject: Re: Re: MMPBSA problem
> Dear amber,
> I re-instal amber and the FE atom is also not recognized. (bad atome FE) I
> used intel compiler, and the _mdread.f _mdread.LES.f files are generated
> (which seems to me that the new mdread.f is acting) .
> I wonder if the new mdread.f should be specified in the shell script?
> (In the attachment, the _mdread.f and _mdread.LES.f are files generated
> after making serial.
> The is shell script, the is input file.
> The md1.log is the log file generated which writes the information of
> error.
> The mdread.f is the new one modified by you.)

Several comments. First, please try upgrading to AmberTools 13 and run
your free energy calculation with that instead.

Also, you are not running correctly in parallel. Just like every other
program in Amber, if you want to run in parallel you have to use the .MPI
version of the software. What you are doing now is just running 4 copies
of the same program that are all running the same analyses and overwriting
each others' files. This is not the cause of your problems, however.

Also, you should _never_ modify the _xxxx.f files (like _mdread.f). These
files are overwritten each time you install, so any changes you make to
those files are discarded. You should modify mdread.f directly.

I think your problem may be fixed just by upgrading to AmberTools 13.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jul 31 2013 - 20:30:03 PDT
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