Hi,
I do not think that your input file is the reason for the run being failed.
You should check if u supplied appropriate restart file ("-c
md_simulation1.rst") and reference file ("-refc file_name.rst(or crd) on the
command line.
Cheers
Zoran
-----Original Message-----
From: Saman Yousuf ali
Sent: Thursday, August 4, 2016 7:16 AM
To: AMBER Mailing List
Subject: [AMBER] error running production with restraint.
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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Received on Thu Aug 04 2016 - 11:30:04 PDT
