Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag

From: Ray Luo <rluo.uci.edu> Date: Mon, 18 Jun 2018 10:07:32 -0700

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Sun, Jun 17, 2018 at 9:57 PM Qing Lv <lvqingjiejie.163.com> wrote:
>
> Hi Colleagues,
>
>
> I am trying to run MMPBSA.py in Amber 18, according to this tutorial:
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section4.htm
> And the input files were also downloaded from this webpage.
> When I ran MMPBSA.py (or MPI version), I got such error messages:
>
>
> /home/amber18/bin/mmpbsa_py_energy: symbol lookup error: /home/amber18/bin/mmpbsa_py_energy: undefined symbol: __libm_feature_flag
>   File "/home/amber18/bin/MMPBSA.py", line 100, in <module>
>     app.run_mmpbsa()
>   File "/home/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File "/home/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/home/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
>     self.prmtop))
> CalcError: /home/amber18/bin/mmpbsa_py_energy failed with prmtop ras-raf.prmtop!
> Exiting. All files have been retained.
>
>
> I did a google search but cannot find useful solutions. Anyone could help?
>
>
> Thanks,
> Qing
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