By the names it looks like atoms 3878 3879 are not bonded
(O2 to H3), but if you look at your system with a molecular
viewer such as VMD using a prmtop you should be able to see
if there is a bond. As Jason suggests, watching each step
unfold using mdcrd should show which atoms are the problem
and may help understand.
Bill
> 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 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
> >
> > 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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Received on Mon Aug 02 2010 - 08:30:05 PDT
