Dear AMBER users,
I’ve tried to calculate the relative binding free energy of my interested system with two ligands.
As I know, in minimization step, the RMS values which is printed out in mdout file are lower than zero when the energy minimization step is finished properly.
But in my case, the RMS values are not lower than zero as below:
| TI region 1
NSTEP ENERGY RMS GMAX NAME NUMBER
999980 -8.8296E+05 1.2437E+01 8.0883E+03 H1 13451
BOND = 55968.9801 ANGLE = 2148.3975 DIHED = 10156.4414
VDWAALS = 96752.3886 EEL = -1081207.2738 HBOND = 0.0000
1-4 VDW = 2822.9485 1-4 EEL = 29822.3032 RESTRAINT = 571.4437
EAMBER = -883535.8147
DV/DL = 10.1473
Softcore part of the system: 13 atoms, TEMP(K) = 0.00
SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 24.0664
SC_BOND= 0.7323 SC_ANGLE= 22.8680 SC_DIHED = 0.4188
SC_14NB= 3.2076 SC_14EEL= 0.3001 SC_VDW = -0.3188
SC_EEL = -3.1415
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 0.9177 SC_VDW_DER= 6.8584 SC_DERIV = 7.7761
------------------------------------------------------------------------------
| TI region 2
NSTEP ENERGY RMS GMAX NAME NUMBER
999980 -8.8296E+05 1.2437E+01 8.0883E+03 H1 13451
BOND = 55968.9801 ANGLE = 2148.3975 DIHED = 10156.4414
VDWAALS = 96752.3886 EEL = -1081207.2738 HBOND = 0.0000
1-4 VDW = 2822.9485 1-4 EEL = 29822.3032 RESTRAINT = 571.4437
EAMBER = -883535.8147
DV/DL = 10.1473
Softcore part of the system: 7 atoms, TEMP(K) = 0.00
SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 1.8493
SC_BOND= 0.0094 SC_ANGLE= 0.2523 SC_DIHED = 0.3976
SC_14NB= 0.0900 SC_14EEL= 1.0523 SC_VDW = -0.1019
SC_EEL = 0.1496
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 0.9177 SC_VDW_DER= 6.8584 SC_DERIV = 7.7761
———————————————————————————————————————
As a result, in NVT step the system blew up, showing the ********** values of energy term as below:
| TI region 2
NSTEP = 542 TIME(PS) = 0.542 TEMP(K) = 579.23 PRESS = 0.0
Etot = -560476.2809 EKtot = 279116.8328 <
tel:2791168328> EPtot = -839593.1138
BOND = 30245.5953 ANGLE = 4898.3676 DIHED = 10516.0007
1-4 NB = 3141.9767 1-4 EEL = 30557.3165 VDWAALS = 149235.4242 <
tel:1492354242>
EELEC = -1070071.5245 EHBOND = 0.0000 RESTRAINT = 1883.7299
EAMBER (non-restraint) = -841476.8436
DV/DL = -9.1920
------------------------------------------------------------------------------
Softcore part of the system: 7 atoms, TEMP(K) = 81.59
SC_Etot= 3.2306 SC_EKtot= 1.2970 SC_EPtot = 1.9336
SC_BOND= 0.0334 SC_ANGLE= 0.6731 SC_DIHED = 0.0840
SC_14NB= 0.0745 SC_14EEL= 1.0373 SC_VDW = -0.1046
SC_EEL = 0.1359
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 6.0181 SC_VDW_DER= -13.2185 SC_DERIV = -7.2004
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
| TI region 1
NSTEP = 543 TIME(PS) = 0.543 TEMP(K) =********* PRESS = 0.0
Etot = ************** EKtot = ************** EPtot = 82273302.2872 <
tel:822733022872>
BOND = 202403.8436 <
tel:2024038436> ANGLE = 5003.6658 DIHED = 10518.9839
1-4 NB = 3166.8943 1-4 EEL = 30754.9640 VDWAALS = 83089630.6340 <
tel:830896306340>
EELEC = -1070079.1504 EHBOND = 0.0000 RESTRAINT = 1902.4521
EAMBER (non-restraint) = 82271399.8351 <
tel:822713998351>
DV/DL = -8.5501
------------------------------------------------------------------------------
Softcore part of the system: 13 atoms, TEMP(K) = 47.32
SC_Etot= 28.3459 SC_EKtot= 1.5516 SC_EPtot = 26.7943
SC_BOND= 0.9114 SC_ANGLE= 23.9108 SC_DIHED = 0.5756
SC_14NB= 3.0850 SC_14EEL= 0.3053 SC_VDW = -0.3191
SC_EEL = -1.6746
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 6.0142 SC_VDW_DER= -12.7633 SC_DERIV = -6.7491
——————————————————————————————————————
Is there any important thing what I’m missing? How to I solve this problem?
Thank you.
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Received on Wed Nov 18 2020 - 23:00:02 PST
