AMBER Archive (2005)

Subject: AMBER: MM_PBSA error

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Mon Apr 11 2005 - 13:46:30 CDT

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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