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-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Tue, Nov 1, 2016 at 1:31 AM, 东不拉 <syd89522.163.com> wrote: > hello: > > 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> > app.run_mmpbsa() > 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 > self.prmtop)) > 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? > > thanks > > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Nov 01 2016 - 11:00:03 PDT