[AMBER] mmpbsa error

From: 东不拉 <syd89522.163.com>
Date: Tue, 1 Nov 2016 16:31:34 +0800 (CST)


when i calculate mmpb(gb)sa via mmpbsa.py, there always show the errors below:

[shangyd.bioserver hc]$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o final_results_mmpbsa.dat -sp mod_wat.prmtop -cp rec-lig.prmtop -rp rec.prmtop -lp lig.prmtop -y mod_wat_md2.mdcrd
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/shangyd/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /home/shangyd/amber14/bin/cpptraj
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/shangyd/amber14/bin/mmpbsa_py_energy
  calculating complex contribution...
/home/shangyd/amber14/bin/mmpbsa_py_energy: symbol lookup error: /home/shangyd/amber14/bin/mmpbsa_py_energy: undefined symbol: __libm_error_support
  File "/home/shangyd/amber14/bin/MMPBSA.py", line 104, in <module>
  File "/home/shangyd/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/shangyd/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/shangyd/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
CalcError: /home/shangyd/amber14/bin/mmpbsa_py_energy failed with prmtop rec-lig.prmtop!
Exiting. All files have been retained.

i have tryed many methods but can not solve this problem. Even if i use the pdb to generate the top files from the tutorial of amber homepage, the error still exists. However, when i use the given top files from tutorial, the calculation is performed normally. i use this command to generate top files: rec-lig= loadpdb "hc.pdb", saveamberparm rec-lig rec-lig.prmtop rec-lig.inpcrd. i modified the pdb files before saving top:pdb4amber -i hc.pdb -o hc1.pdb, the results are totally OK. except mmpbsa.py, mmpbsa.pl, other modules involving top files are normal.

could you tell me how did the errors occur and how can i solve this problem?


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Received on Tue Nov 01 2016 - 02:00:03 PDT
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