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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Tue, Sep 8, 2020 at 3:33 AM Xinye Wang <xywung.163.com> wrote: > Dear Sir/Madam, > > > I calculated mmpb/gbsa of the complex, but there are “nan” words appeared > in the results related to the ligand. > There is no error message in the process of dynamic simulation and > mmpb/gbsa calculation. I would like to know which parameters should I check > or modify? > > > The results are attached as below. > > > GENERALIZED BORN: > > > Complex: > Energy Component Average Std. Dev. Std. Err. of > Mean > > ------------------------------------------------------------------------------- > BOND 1052.9658 28.3502 > 1.4175 > ANGLE 2823.9028 39.8777 > 1.9939 > DIHED 4354.3815 28.6446 > 1.4322 > VDWAALS -2555.2890 26.8711 > 1.3436 > EEL -25263.8169 204.6398 > 10.2320 > 1-4 VDW nan nan > nan > 1-4 EEL nan nan > nan > EGB -4313.7329 159.2503 > 7.9625 > ESURF 132.5119 3.1137 > 0.1557 > > > G gas nan nan > nan > G solv -4181.2210 157.0426 > 7.8521 > > > TOTAL nan nan > nan > > > > > Receptor: > Energy Component Average Std. Dev. Std. Err. of > Mean > > ------------------------------------------------------------------------------- > BOND 1038.0020 28.2286 > 1.4114 > ANGLE 2748.1201 39.9551 > 1.9978 > DIHED 4301.4147 28.7005 > 1.4350 > VDWAALS -2504.0518 25.8072 > 1.2904 > EEL -25068.2159 204.8237 > 10.2412 > 1-4 VDW 1212.0113 14.4160 > 0.7208 > 1-4 EEL 12754.1344 57.7851 > 2.8893 > EGB -4365.1507 160.5109 > 8.0255 > ESURF 135.2085 3.0396 > 0.1520 > > > G gas -5518.5852 195.8649 > 9.7932 > G solv -4229.9421 158.3349 > 7.9167 > > > TOTAL -9748.5274 61.2694 > 3.0635 > > > > > Ligand: > Energy Component Average Std. Dev. Std. Err. of > Mean > > ------------------------------------------------------------------------------- > BOND 14.9638 3.4183 > 0.1709 > ANGLE 75.7827 5.8666 > 0.2933 > DIHED 52.9668 2.1878 > 0.1094 > VDWAALS 2.8750 2.6196 > 0.1310 > EEL -147.1996 5.7474 > 0.2874 > 1-4 VDW nan nan > nan > 1-4 EEL nan nan > nan > EGB -9.0815 1.0634 > 0.0532 > ESURF 3.8031 0.0239 > 0.0012 > > > G gas nan nan > nan > G solv -5.2783 1.0606 > 0.0530 > > > TOTAL nan nan > nan > > > > > Differences (Complex - Receptor - Ligand): > Energy Component Average Std. Dev. Std. Err. of > Mean > > ------------------------------------------------------------------------------- > BOND -0.0000 0.0001 > 0.0000 > ANGLE -0.0000 0.0001 > 0.0000 > DIHED 0.0000 0.0000 > 0.0000 > VDWAALS -54.1122 3.7312 > 0.1866 > EEL -48.4014 5.6393 > 0.2820 > 1-4 VDW nan nan > nan > 1-4 EEL nan nan > nan > EGB 60.4992 4.8246 > 0.2412 > ESURF -6.4998 0.2354 > 0.0118 > > > DELTA G gas nan nan > nan > DELTA G solv 53.9995 4.8830 > 0.2442 > > > DELTA TOTAL nan nan > nan > > > > > -------------------------------------------------------------- > Thank you very much! > > > Sincerely, > > > Xinye Wang > _______________________________________________ > 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 Tue Sep 08 2020 - 12:00:03 PDT