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 Wed Jun 01 2011 - 21:30:02 PDT
