Hi,
You may want to try the script in this repository:
https://github.com/drroe/AmberMdPrep
It implements a protocol for relaxing explicit solvent systems,
detailed here: https://pubmed.ncbi.nlm.nih.gov/32770927
Hope this helps
-Dan
On Thu, Sep 7, 2023 at 3:40 AM KAJAL ABROL via AMBER <amber.ambermd.org> wrote:
>
> 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 - 05:30:02 PDT
