Thank you, Ray.
I recomplied AMBER18 and this time MMPBSA.py works.
At 2018-06-19 01:07:32, "Ray Luo" <rluo.uci.edu> wrote:
>Qing,
>
>First thing first ... Can you run the test cases successfully after
>installation?
>
>All the best,
>Ray
>--
>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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Received on Fri Jun 22 2018 - 21:00:02 PDT
