Hi Jianping,
> I am learning how to use AMBER. When I minimize a protein structure in
> AMBER
> using "maxcyc=200, ncyc-1, imini=1, cut=12.0, igb=1, ntb=0, ntpr=1",
> I got the error "RESTARTED DUE to LINMIN FAILURE" and the output
> coordinate
> with all the number is NaN.
>
> Can someone tell me what it is going on with my simulation and how to
> solve
> it?
Normally LINMIN FAILURE is not a problem but in your case if you are seeing
NaN this likely means some value is infinite. This generally occurs because
of a divide by zero. Probably because of a bad starting structure. You
likely have two atoms sitting on top of each other. You should check your
starting structure carefully. Note, ptraj has a facility to help with this
(checkoverlap???). You should also look at the atom printed on the first
energy line of the minimization. Next to the GMAX value. This is the atom
with the largest force on it and quite likely will be the source of your
problem.
Good luck,
Ross
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| San Diego Supercomputer Center |
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Received on Wed Aug 19 2009 - 20:19:08 PDT
