AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA error

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Mon Apr 11 2005 - 15:49:37 CDT


Hi,

I think the problem is that the sander version that is called by mm_pbsa
is the parallel version, which requires to set "mpirun" or the like in
front of the sander call. You should be able to circumvent this by
adding a line "SANDER <path_to_a_one_processor_version_of_sander>" to
the end of the mm_pbsa.in file (in the section @PROGRAMS).

Best regards

Holger

Xin Hu schrieb:

Dear Amber user

I have a problem with the MM_PBSA calculation. I followed the examples
in /src/mm_pbsa/example/02_MMPBSA_Stability to run the calculation on
entropy energies,

it showed an error:

=>> Calculating energy / entropy contributions
    Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1
        Calc MM/GB/SAS

  Unit 6 Error on OPEN: sander_com.1.out
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_14716: p4_error: : 1
        /usr/local/amber8/exe/sander -O -i sander_com.in -o
sander_com.1.out -c ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1 -p
../ras_raf_II_wt.prmtop not successful

I was aware that if I ingore the path specified in the command, or I add
the full path (the working directory) to the output files, it works
properly.

So I tried to modify the script in src/mm_pbsa, the script
"mm_pbsa_util.pm" or "mm_pbsa_calceneent.pm", attemping to delete the
path associated with command "sander", or adding

path to the output file, however, neither way is working with errors
showing "compilation failed" "strict subs" etc.

I wonder if anyone has caught the same problem and I appreciate for
help. The Amber8 is runnung on a linux cluster with MPI on parallel.

Thanks,

Xin
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu