Hi Ross
Sorry for the late reply. Thanks a lot for the help. It solves my problem.
Jianping
On Mon, Aug 3, 2009 at 12:38 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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Received on Wed Aug 19 2009 - 20:58:30 PDT
