looking at the energy after 400 steps is difficult to evaluate, but since
the energy is very large and negative and the vdw energy is not that high,
I would guess that you have a parameter problem. overlapping atoms should
give very high vdw energies. you'll need to look at your parameters and the
antechamber output to see what's going on.
it also might help to look at the inositol by itself since that will be
faster to debug than including protein and water too.
On Wed, May 13, 2015 at 7:08 AM, anu chandra <anu80125.gmail.com> wrote:
> 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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>
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Received on Wed May 13 2015 - 05:00:02 PDT
