Generate the pdb from the finally prepared parameter and trajectories files
using ambpdb command usage. Then check the atom *NZ 2524* in detail. I
guess it is the culprit having something unusual.
Hirdesh
On Thu, Jun 2, 2011 at 9:31 AM, Praapti Jayaswal <praapti.gmail.com> wrote:
> Hi All,
>
> I am trying to run energy minimization on a protein structure . when i run
> sander it hangs-up after a few seconds and the minimization output file
> shows :
>
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 682125
> | TOTAL SIZE OF NONBOND LIST = 5264395
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 6.4218E+09 7.2626E+08 1.1426E+11 NZ 2524
>
> BOND = 123.8350 ANGLE = 415.5306 DIHED =
> 2022.1738
> VDWAALS = ************* EEL = -102078.8972 HBOND =
> 0.0000
> 1-4 VDW = 1110.2078 1-4 EEL = 9602.0933 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 5 2.6812E+09 2.7188E+08 4.2715E+10 NZ 2524
>
> BOND = 124.1428 ANGLE = 415.7048 DIHED =
> 2022.1812
> VDWAALS = ************* EEL = -102085.9218 HBOND =
> 0.0000
> 1-4 VDW = 1110.2274 1-4 EEL = 9602.0919 RESTRAINT =
> 0.0007
> EAMBER = *************
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10 3.7322E+08 2.5957E+07 3.7425E+09 NZ 2524
>
> BOND = 128.7875 ANGLE = 417.6624 DIHED =
> 2022.2293
> VDWAALS = ************* EEL = -102100.4695 HBOND =
> 0.0000
> 1-4 VDW = 1110.3050 1-4 EEL = 9602.0830 RESTRAINT =
> 0.0107
> EAMBER = *************
>
>
> The minimization doesn't run beyond this. Could you please help, I am new
> to
> AMBER.
>
> Thanks in advance,
>
> Praapti
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Received on Thu Jun 02 2011 - 02:00:03 PDT
