Dear AMBER Community,
I am getting an error[1] upon performing minimization of drug-protein complex by using the AMBER tutorial[2].
There seems to be nothing wrong with the complex as per visual inspection of complex PDB file obtained after parametrization.
Please let me know if sharing the output file can be more helpful.
Thank you very much.
[1]
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 9.2217E+09 O1 18
BOND = 13750.1241 ANGLE = 10976.5308 DIHED = 2934.9414
VDWAALS = NaN EEL = Infinity EGB = 60228.2741
1-4 VDW = 381037.7111 1-4 EEL = 14860.5376 RESTRAINT = 0.0000
.
.
.
.
.
NSTEP ENERGY RMS GMAX NAME NUMBER
2519 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2520 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2521 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2521 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
[2]
https://ambermd.org/tutorials/basic/tutorial4b/index.php
——
Jatin Kashyap
Ph.D. Student
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu
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Received on Tue Jan 05 2021 - 17:00:02 PST
