Thank you so much
I will check all these things
Regards,
kamlesh
On Mon, Apr 26, 2010 at 7:50 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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>
--
Kamlesh Kumar Sahu (Ph.D. student)
Dept. of applied chemistry, Tohoku University graduate school of
engineering, Aoba-yama, Sendai
JAPAN
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Received on Mon Apr 26 2010 - 18:00:04 PDT
