It will probably help to visualize your trajectory to see what's going on.
Write out coordinate snapshots every step (ntwx=1), and run for 10 steps
(since the error occurs on step 9), and take a look at any potential problem
areas.
Also, what is the gradient of your final minimization? Is it properly
minimized? What is the reference structure in your heating? Is it the same
as the input coordinates for the simulation?
All the best,
Jason
On Mon, Aug 2, 2010 at 2:22 AM, rameshwar prajapati <
rameshwar.niper.gmail.com> wrote:
> sir what correction i should make i am not getting
>
>
> ATOM 3853 C10 OTC 232 -10.947 -4.843 2.161 1.00 0.00
> ATOM 3854 C11 OTC 232 -10.084 -4.220 1.248 1.00 0.00
> ATOM 3855 H17 OTC 232 -9.073 -3.946 1.551 1.00 0.00
> ATOM 3856 H16 OTC 232 -10.595 -5.069 3.168 1.00 0.00
> ATOM 3857 C9 OTC 232 -12.261 -5.179 1.794 1.00 0.00
> ATOM 3858 Cl1 OTC 232 -13.355 -5.759 2.998 1.00 0.00
> ATOM 3859 C8 OTC 232 -12.692 -4.956 0.472 1.00 0.00
> ATOM 3860 H15 OTC 232 -9.106 -3.906 1.581 1.00 0.00
> ATOM 3861 C7 OTC 232 -11.825 -4.343 -0.456 1.00 0.00
> ATOM 3862 H14 OTC 232 -10.621 -4.997 3.175 1.00 0.00
> ATOM 3863 C6 OTC 232 -10.527 -3.948 -0.061 1.00 0.00
> ATOM 3864 C5 OTC 232 -9.666 -3.094 -0.965 1.00 0.00
> ATOM 3865 2H1 OTC 232 -12.181 -4.126 -1.452 1.00 0.00
> ATOM 3866 3H1 OTC 232 -13.701 -5.211 0.185 1.00 0.00
> ATOM 3867 C4 OTC 232 -8.211 -3.554 -1.156 1.00 0.00
> ATOM 3868 H10 OTC 232 -9.674 -2.107 -0.506 1.00 0.00
> ATOM 3869 1H1 OTC 232 -10.145 -2.971 -1.937 1.00 0.00
> ATOM 3870 C3 OTC 232 -7.302 -2.386 -1.550 1.00 0.00
> ATOM 3871 H8 OTC 232 -8.186 -4.327 -1.924 1.00 0.00
> ATOM 3872 H9 OTC 232 -7.808 -4.016 -0.255 1.00 0.00
> ATOM 3873 O3 OTC 232 -6.978 -1.617 -0.398 1.00 0.00
> ATOM 3874 N1 OTC 232 -7.143 -0.233 -0.603 1.00 0.00
> ATOM 3875 S1 OTC 232 -8.591 0.563 -0.390 1.00 0.00
> ATOM 3876 O1 OTC 232 -9.117 0.196 0.900 1.00 0.00
> ATOM 3877 H2 OTC 232 -3.971 0.192 -0.051 1.00 0.00
> ATOM 3878 O2 OTC 232 -9.388 0.363 -1.573 1.00 0.00
> ATOM 3879 H3 OTC 232 -4.916 -1.176 0.044 1.00 0.00
> ATOM 3880 N2 OTC 232 -8.170 2.166 -0.334 1.00 0.00
> ATOM 3881 H1 OTC 232 -8.967 2.778 -0.117 1.00 0.00
> ATOM 3882 C1 OTC 232 -6.856 2.565 -0.517 1.00 0.00
> ATOM 3883 N5 OTC 232 -6.642 3.873 -0.694 1.00 0.00
> ATOM 3884 H6 OTC 232 -7.798 -1.788 -2.317 1.00 0.00
> ATOM 3885 H7 OTC 232 -6.372 -2.775 -1.967 1.00 0.00
> ATOM 3886 N3 OTC 232 -5.875 1.759 -0.503 1.00 0.00
> ATOM 3887 C2 OTC 232 -5.944 0.492 -0.498 1.00 0.00
> ATOM 3888 N4 OTC 232 -4.797 -0.278 -0.410 1.00 0.00
> ATOM 3889 H4 OTC 232 -7.432 4.518 -0.720 1.00 0.00
> ATOM 3890 H5 OTC 232 -5.700 4.241 -0.677 1.00 0.00
>
> please tell
> thanks
>
> On Mon, Aug 2, 2010 at 11:26 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > deviation is too large
> > > NITER, NIT, LL, I and J are : 0 2 1945 3878 3879
> >
> > You should look at atoms 3878 3879 in your structure.
> >
> > Bill
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 02 2010 - 05:00:09 PDT
