Good Morning,
I am new to AMBERTOOLS and I just installed the latest version of
AMBERTOOLS (AmberTools13).
I compiled only AMBERTOOLS13 without problems. However 2 tests
(01_Generalized_Born and 03_Alanine_Scanning) resulted in an error.
Hereafter you will find part of the *.log and the mmpbsa.out for
03_Alanine_Scanning (the problem seems to be the same for
01_Generalized_Born).
Any suggestions would be appreciated.
Thank you
Kind Regards
Marco
from *.log
cd mmpbsa_py && make test
make[3]: Entering directory `xxx/AmberTools/test/mmpbsa_py'
cd EstRAL_Files && ./Run.makeparms
diffing com.top with c.top
PASSED
...
cd 01_Generalized_Born && ./Run.GB
./Run.GB: Program error
make[3]: *** [GB] Error 1
cd 02_Poisson_Boltzmann && ./Run.PB
diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
PASSED
==============================================================
diffing energies.csv.save with energies.csv
PASSED
==============================================================
cd 03_Alanine_Scanning && ./Run.ALA
./Run.ALA: Program error
make[3]: *** [ALA] Error 1
cd 04_Per_Residue_Decomp && ./Run.PerRes
This test requires sander and can only be run with Amber12 installed.
from mmpbsa.out
Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
Mutating trajectories...
2 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
xxx/ambertools/ambertools13/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
File "xxx/ambertools/ambertools13/amber12/bin/MMPBSA.py", line 91, in
<module>
app.run_mmpbsa()
File "xxx/ambertools/ambertools13/amber12/bin/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"xxx/ambertools/ambertools13/amber12/bin/MMPBSA_mods/calculation.py",
line 78, in run
calc.setup()
File
"xxx/ambertools/ambertools13/amber12/bin/MMPBSA_mods/calculation.py",
line 195, in setup
raise IOError("Input file (%s) doesn't exist" % self.input_file)
IOError: Input file (_MMPBSA_gb.mdin) doesn't exist
Exiting. All files have been retained.
mmpbsa_py_energy found! Using
xxx/ambertools/ambertools13/amber12/bin/mmpbsa_py_energy
cpptraj found! Using xxx/ambertools/ambertools13/amber12/bin/cpptraj
--
********************************************
Marco Molinari
Research Officer
Department of Chemistry
University of Bath
Claverton Down
Bath BA2 7AY
United Kingdom
Email: m.molinari.bath.ac.uk
Telephone: 0044 (0)1225 386523
Office 1.19, Building 1S
********************************************
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Received on Thu Oct 24 2013 - 04:00:02 PDT
