What is the command line you used to execute the simulation? When
using positional restraints you need to specify reference coordinates
with the '-ref' flag. Make sure that file can be opened by e.g.
reading it into cpptraj.
-Dan
On Wed, Aug 3, 2016 at 11:16 PM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> Dear all,
> After minimization and equilibration steps using amber14 package, I want to run 5ns production by applying restraint on some part (268-532 residues) of my target protein, total residues 1-532 residues. I have used the following input file:
> polyA-polyT 10-mer: 100ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 1,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 2500000, dt = 0.002,
> ntpr = 1000, ntwx = 500, ntwr = 1000
> restraintmask = ':268-532.CA,C,N', restraint_wt = 5.0, /
> I got this error,
> Starting Script at: Thu Aug 4 17:58:27 PKT 2016
>
> Job 1 started at: Thu Aug 4 17:58:27 PKT 2016
>
> Unit 10 Error on OPEN: refc
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> gzip: md_simulation1.mdcrd: No such file or directory
> Job 1 finished at: Thu Aug 4 17:58:28 PKT 2016
> Job 2 started at: Thu Aug 4 17:58:28 PKT 2016
>
> Unit 9 Error on OPEN: md_simulation1.rst
>
> Is there any mistake in my input file?
> Thanks in advance.
>
> Best Regards, Saman Yousuf Ali
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Aug 04 2016 - 08:30:03 PDT
