Hello,
>
> I'm trying to do a NMA for a 170 residue long protein, and I wanted to do
> the nmode minimization beforehand. I saw that someone had this "bad nonbon"
> error before, but I didn't see a response. It seems like nmode is quitting
> before it can do any minimization steps. I have tried using a structure
> minimized with sander, and then minimizing with nmode, but this causes the
> same error. If I change drms to a number larger than the first minimization
> step, then it will do the NMA, but I'm just skipping the minimization then.
> Here is the output from nmode:
>
>
> ntrun maxcyc ibelly drms
> 4 10000 0 0.10E-04
> rcut scnb scee dielc idiel
> 99.00000 2.00000 2.00000 1.00000 0
> nsave dfpred bdwnhl smx emx alpha ndiag
> 1 0.01000 0.10000 0.08000 0.30000 0.80000 10
> ipol = 0
> i3bod = 0
> nvect = 20
>
> Total memory required : 60022027 real words
> Total memory required : 3491011 integer words
> Total memory required : 7913 4-character words
>
> Maximum nonbond pairs 3324330
>
> Duplicated 0 dihedrals
> Duplicated 0 dihedrals
>
> Number of non-bonded pairs = 3310381
> Number of H-bonded pairs = 0
>
> ***************** ***************** *****************
> step = 0
> F = -0.117597E+04 GRDMAX = 0.124782E+03 GNORM = 0.182217E+02
> E-NONB E-ELE E-HBOND E-BOND
> -0.12053E+04 -0.52976E+04 0.00000E+00
> 0.48824E+03
> E-ANGLE E-DIHED E-NB14 E-EEL14
> 0.13396E+04 0.17020E+04 0.61843E+03
> 0.11786E+04
> E-POL E-3BOD
> 0.00000E+00 0.00000E+00
> Coordinate origin is now the molecular center of mass
> b1 = -9.26200 b2 = -6.72184 tlamba = -9.36200
> rms of step length = 0.0734066686
> Bad nonbon: 1 14 0.90176E+00 0.42153E+03
> Bad nonbon: 1 15 0.14470E+01 0.22426E+05
> Bad nonbon: 1 23 0.39872E+01 0.11226E+03
> Bad nonbon: 1 24 0.14262E+01 0.14649E+05
> Bad nonbon: 1 25 0.11928E+00 0.39683E+09
> Bad nonbon: 1 26 0.56749E+00 0.30205E+04
> Bad nonbon: 1 27 0.26163E+01 0.11753E+04
> Bad nonbon: 1 42 0.24957E+01 0.14220E+04
> Bad nonbon: 1 43 0.79688E+00 0.72413E+03
> Bad nonbon: 1 44 0.45262E+01 0.63612E+02
> Bad nonbon: 1 46 0.18131E+01 0.75036E+04
> ...
> Bad bond: 907 908 0.38897E+01 0.96000E+00 0.55300E+03 0.47464E+04
> ene .step k-1 = -1175.967735 ene .k = ***************
> Bad nonbon: 1 14 0.92584E+00 0.37506E+03
> ...
> Bad nonbon: 1129 1154 0.10589E+00 0.37033E+05
> Bad nonbon: 1130 1148 0.56320E+00 0.87146E+02
> ene .step k-1 = -1175.967735 ene .k = ***************
> ... scaling was unsuccessful ... stop
>
>
> Thanks,
> Jeremy Harris
>
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Received on Tue Jan 06 2009 - 15:29:54 PST
