this means that the system is unstable.
my guess is that you have used non-standard force field parameters but have
forgotten to tell us.
if yes, search the amber web site for the error message. you will see lots
of discussion about the error and advice to people that created new
parameters.
If it is completely standard Amber parameters, the tell us how you built the
structure. The minimizer can handle most problems, but maybe you built a
structure that cannot be fixed (knotted rings, overlapped packing). The best
thing to do is to look at the atom under "GMAX NAME NUMBER" at step 1 and
then use a visualization program to see what is wrong at that spot.
On Mon, Apr 26, 2010 at 4:31 AM, kamlesh sahu <kamleshsemail.gmail.com>wrote:
> hello amber users,
> I am new user. When I tried to minimize one structure, I got following
> message.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10000 -8.6148E+07 5.1600E+11 5.2770E+13 H2 10140
>
> BOND = 955.1086 ANGLE = 1159.3031 DIHED =
> 4954.8413
> VDWAALS = -2911.0127 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 1788.4797 1-4 EEL = 19090.7988 RESTRAINT =
> 0.6814
> EAMBER = *************
> Frac coord min, max: -8439365.76177023 8439367.24932251
> 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
> "min.out" 1045L, 47424C
>
> The input file was this -
>
> title
> &cntrl
> imin=1,ntmin=1,
> maxcyc=20500, ncyc=10000,
> ntpr=1
> scee=1.2, scnb=2.0,
> nsnb=999999,
> ntb=0,
> cut=12,
> fcap=1,
> &end
>
>
> Could you please tell me what it means ?
>
> Regards,
> k
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 26 2010 - 04:00:04 PDT
