Dear AMBER community,
I was following the
https://ambermd.org/tutorials/basic/tutorial13/index.php link for the
Relaxation of the explicit water system, and my protein showed some of the
energies with ************* in the minimization output file.
I used this minimization script:
minimization of solvent
&cntrl
imin = 1, maxcyc = 1000,
ncyc = 1000, ntx = 1,
ntwe = 0, ntwr = 500, ntpr = 50,
ntc = 1, ntf = 1, ntb = 1, ntp = 0,
cut = 10.0,
ntr=1, restraintmask = ':1-173',
restraint_wt = 100.,
ioutfm=1, ntxo=2,
/
*The output file : *
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 = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 6472115
| TOTAL SIZE OF NONBOND LIST = 6472115
NSTEP ENERGY RMS GMAX NAME NUMBER
1 5.9468E+11 6.3298E+10 3.9362E+12 O 12349
BOND = 17301.3526 ANGLE = 1721.3436 DIHED =
2803.4318
VDWAALS = ************* EEL = -44451.1195 HBOND =
0.0000
1-4 VDW = 3094.4584 1-4 EEL = 15098.6997 RESTRAINT =
0.0000
CMAP = 411.8784
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -3.9085E+04 5.0489E+00 4.2231E+02 H1 14610
BOND = 1503.5604 ANGLE = 1589.3263 DIHED =
2826.1472
VDWAALS = -6137.8096 EEL = -56886.6703 HBOND =
0.0000
1-4 VDW = 2846.6460 1-4 EEL = 14475.2994 RESTRAINT =
313.2278
CMAP = 385.2284
EAMBER = -39398.2722
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -5.0724E+05 2.9488E+06 4.6334E+08 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0356 EEL = -524579.4665 HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = -507539.9116
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -2.0026E+08 7.1445E+11 1.1332E+14 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -8.5386E+07 1.2971E+11 2.0574E+13 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
250 -3.3762E+08 2.0316E+12 3.2225E+14 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -3.6502E+07 2.3627E+10 3.7476E+12 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
350 -2.3796E+08 1.0089E+12 1.6004E+14 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -4.3236E+07 3.3178E+10 5.2626E+12 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
450 -1.6490E+08 4.8431E+11 7.6820E+13 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -2.1893E+07 8.4669E+09 1.3430E+12 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -6.3038E+07 7.0634E+10 1.1204E+13 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -2.4750E+08 1.0915E+12 1.7314E+14 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
650 -9.3609E+07 1.5593E+11 2.4733E+13 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -3.4165E+09 2.0816E+14 3.3017E+16 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
750 -3.4625E+07 2.1253E+10 3.3711E+12 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
800 -1.3225E+08 3.1144E+11 4.9400E+13 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
850 -1.4061E+08 3.5206E+11 5.5844E+13 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
900 -8.6372E+07 1.3272E+11 2.1053E+13 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
950 -2.1206E+07 7.9415E+09 1.2597E+12 Na+ 11210
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -8.2027E+07 1.1969E+11 1.8985E+13 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -8.2027E+07 1.1969E+11 1.8985E+13 O4 11208
BOND = 1606.2378 ANGLE = 1555.5847 DIHED =
2842.7220
VDWAALS = -6450.0357 EEL = ************* HBOND =
0.0000
1-4 VDW = 2763.9461 1-4 EEL = 14336.4161 RESTRAINT =
300.0873
CMAP = 384.6839
EAMBER = *************
*Please suggest me any solution for rectifying this issue.*
Thanks and Regards,
Kajal Abrol
Research Scholar
Department of Bioinformatics
Pondicherry University
Puducherry
India
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Received on Thu Sep 07 2023 - 01:00:02 PDT
