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
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Received on Mon Apr 11 2005 - 22:53:00 PDT
