On Fri, Aug 10, 2012 at 4:01 PM, Zalikha Ibrahim
<zalikha.ibrahim.yahoo.com>wrote:
> Hi to all,
>
> I tried to perform minimization on a protein. My input file is as below:
>
> Protein initial minimization with 8A cutoff
> &cntrl
> imin = 1,
> ncyc = 500,
> maxcyc = 1000,
> ntr = 1,
> ntb = 1,
> cut = 8.0,
> ntpr = 50,
> /
>
> Don't leave this blank line.
> keep protein fixed with restraint
> 500.0
> RES 1 668
> END
> END
>
> /
>
You don't need this "/" either.
Terry
>
> The sander command was:
> sander -O -i min1a1.in -o min1a1.out -p prot_solv.prmtop -c
> prot_solv.inpcrd -r min1a1.rst -ref prot_solv.inpcrd
>
>
> It didn't proceed, and gave this response:
>
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
>
> When I checked the .out file, it showed these messages:
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
>
>
>
> rfree: Error decoding variable 1 3 from:
> keep
>
> this indicates that your input contains
>
> incorrect information
>
> field 1 was supposed to
>
> have a (1=character, 2=integer, 3=decimal) value
>
>
> Would anyone tell me what is this means and what am i suppose to do to
> make it right? Did I use the correct input file?
> Thanks in advance
>
> Zalikha Ibrahim
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Received on Fri Aug 10 2012 - 01:30:08 PDT
