Dear Amber community,
During the minimization of protein, the VDw and ELE are showing asterisk
(*) values meaningly that the virtual box for calculating energy is
exceeded by 30 Angstrom. I am giving the input as well as output file
glimpse below. Any help will be appreciated.
*Input*
initial minimisation of solvent
&cntrl
imin=1, maxcyc=20000, ntmin = 2,
ntx = 1, ntc = 1, ntf = 1,
ntb = 1, ntp = 0, ncyc = 500,
ntwx = 250, ntpr = 250,
ntr = 1, cut = 10.0
/
Hold the protein fixed
500.0
RES 1 193
END
END
*Output glimpse*
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -1.0356E+08 3.1570E+11 9.1527E+13 H2 4910
BOND = 14319.4400 ANGLE = 804.5621 DIHED =
3642.3795
VDWAALS = 24359.9107 EEL = -292615.4049 HBOND =
0.0000
1-4 VDW = 1067.0455 1-4 EEL = ************* RESTRAINT =
43.0606
EAMBER = *************
Thanks
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Received on Mon Apr 08 2024 - 03:30:02 PDT
