Dear Amber users,
I am working with simulation of protein which bound to Inositiol-1,4,5-
triphosphate (IP3). I have derived the IP3 force field parameters using
antechamber and ESP charges from QM calculations using Gaussian 09.
Unfortunately, I failed with the very first in-vacuum minimization itself.
The portion of minimization steps are shown below.
*****************************************************************************************
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -3.5490E+07 3.6422E+10 3.6367E+12 O42 9582
BOND = 866.9863 ANGLE = 1709.9765 DIHED =
7301.5077
VDWAALS = -2445.4775 EEL = ************* HBOND =
0.0000
1-4 VDW = 2978.7278 1-4 EEL = 25591.9838 RESTRAINT =
392.4443
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
450 -1.3162E+08 5.0104E+11 5.0028E+13 H8 9589
BOND = 866.9890 ANGLE = 1709.9765 DIHED =
7301.5077
VDWAALS = -2445.4755 EEL = ************* HBOND =
0.0000
1-4 VDW = 2978.7278 1-4 EEL = 25591.9837 RESTRAINT =
392.4446
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -1.7765E+07 9.1225E+09 9.1087E+11 H8 9589
BOND = 866.9928 ANGLE = 1709.9767 DIHED =
7301.5077
VDWAALS = -2445.4728 EEL = ************* HBOND =
0.0000
1-4 VDW = 2978.7278 1-4 EEL = 25591.9835 RESTRAINT =
392.4448
EAMBER = *************
Frac coord min, max: -2376266.4674540758 2376267.6814063941
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
******************************************************************************************
I have noticed that the atoms O42 and H8 got overlapped, though they look
fine in the starting structure.My trials with alternative steps by putting
restrains on atoms/molecules also failed.
Please provide your expert suggestions to get rid off these issues.
Many thanks in advance
Anu
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Received on Wed May 13 2015 - 04:30:03 PDT
