Zalikha's advice is correct.
You can also use "restraintmask" to select the atoms you wish to restrain
-- it is less picky than the GROUP input and more flexible when it comes to
atom selection (there are still some things you can only do via group
input, but what you're trying to do is trivial with a restraintmask).
HTH,
Jason
On Fri, Aug 10, 2012 at 4:06 AM, Terry <terrencesun.gmail.com> wrote:
> 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
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 10 2012 - 06:00:05 PDT
