Dear All,
It seems everything is correct. I am not able to know where the problem is.
The command I used is
mpirun -perhost 16 -np 128 ~/softwares/amber14/bin/sander.MPI -O -i
eq_nvt.in -p UVI_DNA_Mg_Na_Sol_after_miz3.prmtop -c system_EM.rst -r
eq_nvt.rst -o eq_nvt.out -x eq_nvt.mdcrd -inf eq_nvt.info
Last few lines of system_EM.rst file
9.3683764 12.0844517 15.0382198 8.6494519 12.8704741 13.9743196
16.0011108 11.2811455 14.1604478 16.6792008 10.5808002 14.2140069
16.2855876 11.8563769 14.9115764
My en_nvt.in file
Equilibration NVT with restraints on protein 20ps
&cntrl
imin = 0,
irest = 0,
ig = -1,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
&ewald
order = 4,
/
Keep protein fixed with weak restraints
10.0
RES 1 126
END
END
Thank you so much.
Sincerely,
Sunita
On Thu, Apr 9, 2020 at 5:20 PM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Apr 09, 2020, Sunita Patel wrote:
>
> > getting new box info from bottom of inpcrd
> >| INFO: Old style inpcrd file read
> >
> >| peek_ewald_inpcrd: Box info not found in inpcrd
>
> Look at the last line of your inpcrd file: does it have box information?
>
> Double-check your filenames: a common cause of this message is that you
> gave some other file than the restart file from the minimization as the
> file named in the -c flag.
>
> ....dac
>
>
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Received on Thu Apr 09 2020 - 06:30:02 PDT
