[AMBER] problem with MM/PB(GB)SA (Geng Dong)

From: <gdong.stu.edu.cn>
Date: Tue, 5 Nov 2019 08:21:53 +0000

Dear all,

I have been trying to run MMPBSA.py on AMBER18 using one core and I am confused with two problems showed below.
The first question is about the GBSA. GB calculation failed with PL.prmtop (protein with ligand). The calcerror showed the cpptraj failed with prmtop PL.prmtop, which was quite similar to a problem showed by Jag I saw on your website http://archive.ambermd.org/201602/0177.html. I checked the output file(_MMPBSA_complex_gb.mdout.0) and it printed MM/GBSA processing done! It stopped on this step and I found the value of esurf is zero indicating the surface area was failing in cpptraj as you had said on the amber mailing. In the end I still cannot find what reason caused this problem and how to solve it.

Information in detail:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/Geng/Program/amber18/bin/mmpbsa_py_energy
cpptraj found! Using /home/Geng/Program/amber18/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/Geng/Program/amber18/bin/mmpbsa_py_energy
  calculating complex contribution...
  File "/home/Geng/Program/amber18/bin/MMPBSA.py", line 100, in <module>
    app.run_mmpbsa()
  File "/home/Geng/Program/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/Geng/Program/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/Geng/Program/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 478, in run
    self.prmtop))
CalcError: /home/Geng/Program/amber18/bin/cpptraj failed with prmtop PL.prmtop!
Exiting. All files have been retained.


The second question is about the PB. According to the description of Jag, I also calculated PB alone and it succeeded as well while the result (MMPBSA.dat) was quite weird comparing to a normal one. The energy difference of BOND was quite large and the result of ANGLE was nan.

WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 6989927.5966 4302005.2073 192391.5217
ANGLE nan nan nan
DIHED 4734.9672 24.0139 1.0739
VDWAALS -3074.5516 25.0129 1.1186
EEL -24965.3966 115.5749 5.1687
1-4 VDW 1354.1557 15.1246 0.6764
1-4 EEL 14320.6802 50.0816 2.2397
EPB -4946.9619 93.1503 4.1658
ENPOLAR 92.3966 1.0545 0.0472

G gas nan nan nan
G solv -4854.5653 92.6190 4.1420

TOTAL nan nan nan


Could you give me some suggestions?

I would be very grateful for your help.

Geng

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Received on Tue Nov 05 2019 - 00:30:02 PST
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