There is probably no error. If you look through the output to find ioutfm,
you'll see that it defaults to 1, which means "write NetCDF restarts." The
gobbledegook you see there is a binary representation of the coordinates.
Try restarting a run from that restart file--it should work fine. If you
want to be able to read the coordinates in your restart and .crd files, add
"ioutfm = 0" to the input.
Dave
On Wed, Jun 12, 2019 at 2:13 PM Yuwei Song <songyw1991.gmail.com> wrote:
> Hi Amber
> I was using sander for a complex minimization under Amber 18.
> The out file did not show any error, however, the rst file generated showed
> messy code.
> Here is my in file
>
> vi min-complex.in
>
> =====BEGINNING OF FILE =====
>
> JOB: Initial Minimization of Protein Complex
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 500, dx0 = 0.005
> ntf = 1, ntb = 0,
> cut = 10.0, nsnb = 20,
> ntr = 0,
> &end
>
> ===== END OF FILE =====
>
> sander -O -i min-complex.in -p 5AVIVDB.prmtop -c 5AVIVDB.inpcrd -ref
> 5AVIVDB.inpcrd -o min-complex.out -r 5AVIVDB-min.inpcrd -x
> 5AVIVDB-min.mdcrd -inf 5AVIVDB-min.mdinfo
>
> I also attached my .out file. Please help me figure out where is going
> wrong?
> Thank you very much
>
> --
>
> Scholar, Dr. Andrzej Slominski Laboratory
> Dept. of Dermatology
> The University of Alabama at Birmingham
> Phone: (205) 447-9238
> Email:songyw.uab.edu <Email%3Ayhsong.uab.edu>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 12 2019 - 13:00:03 PDT
