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
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Received on Tue Sep 08 2020 - 04:00:03 PDT
