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-- 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 Tue, Nov 5, 2019 at 12:23 AM 东庚 <gdong.stu.edu.cn> wrote: > > 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 > > _______________________________________________ > 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 Wed Nov 06 2019 - 09:30:02 PST