Re: [AMBER] mmpbsa error

From: Ray Luo <>
Date: Tue, 1 Nov 2016 10:35:45 -0700

Apparently your own prmtop files do not match the structure files. To
confirm, load these files into vmd to see whether you can see anything

To debug this, in an empty folder, use leap to save these files again
and share with us the leap.log file.

Ray Luo, Ph.D.
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 <> wrote:
> hello:
> when i calculate mmpb(gb)sa via, there always show the errors below:
> [shangyd.bioserver hc]$ $AMBERHOME/bin/ -O -i -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/", line 104, in <module>
>     app.run_mmpbsa()
>   File "/home/shangyd/amber14/lib/python2.7/site-packages/MMPBSA_mods/", line 218, in run_mmpbsa
>, self.stdout)
>   File "/home/shangyd/amber14/lib/python2.7/site-packages/MMPBSA_mods/", line 82, in run
>, stdout=stdout, stderr=stderr)
>   File "/home/shangyd/amber14/lib/python2.7/site-packages/MMPBSA_mods/", 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,, 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 mailing list
Received on Tue Nov 01 2016 - 11:00:03 PDT
Custom Search