Try typing
ls -la mden
Maybe you don't have write permission. This is more of a Unix system issue
than Amber. For now giving it a different file name on the pmemd command
line should work..
On Mon, Jan 18, 2021, 7:07 PM Jatin Kashyap <jk435.njit.edu> wrote:
> I can see one file called mden in my current directory.
> I had run the previous steps i.e. minimization & heating, in the same
> directory; nothing else.
>
> There are 1010 lines in that mden file. I am not able to find out whether
> those lines are from eq.in run or from previous.
> I can share the file here if you think it can help.
>
> Thank you.
>
> ——
> Jatin Kashyap
> Ph.D. Student
> Dr. Dibakar Datta Group
> Department of Mechanical and Industrial Engineering
> New Jersey Institute of Technology (NJIT)
> University Heights
> Newark, NJ 07102-1982
> Phone- (201)889-5783
> Email- jk435.njit.edu
>
> > On Jan 18, 2021, at 7:01 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
> >
> > You can try that, but it should work with the default. Is there a file
> > called mden in that directory with the other outputs?
> >
> > On Mon, Jan 18, 2021, 6:48 PM Jatin Kashyap <jk435.njit.edu> wrote:
> >
> >> Please look below for the job script.Yes, I do have the permission to
> >> write in that directory. Shall I just add -e with a file name?
> >>
> >>
> >>
> >> module unload intel
> >> module load amber
> >>
> >> pmemd -i eq.in -o eq.out -p dna.prmtop -c heat.rst -r eq.rst -x
> eq.mdcrd
> >> -ref heat.rst
> >>
> >> ——
> >> Jatin Kashyap
> >> Ph.D. Student
> >> Dr. Dibakar Datta Group
> >> Department of Mechanical and Industrial Engineering
> >> New Jersey Institute of Technology (NJIT)
> >> University Heights
> >> Newark, NJ 07102-1982
> >> Phone- (201)889-5783
> >> Email- jk435.njit.edu
> >>
> >>> On Jan 18, 2021, at 6:43 PM, Carlos Simmerling <
> >> carlos.simmerling.gmail.com> wrote:
> >>>
> >>> please send the job script where you specified the file names.
> >>> you specify ntwe=500, which means to write energy values. The job
> script
> >>> will have the name of the file that you want to write energies,
> following
> >>> the -e flag (see the Amber manual for details). If you don't specify
> it,
> >>> mden is the default. Do you have permission to write in the directory
> >> where
> >>> you are running this? you might try adding -e with a file name to the
> >> pmemd
> >>> command line.
> >>>
> >>> On Mon, Jan 18, 2021 at 6:32 PM Jatin Kashyap <jk435.njit.edu> wrote:
> >>>
> >>>> Please look for mini.in[1], heat.in[2], and eq.in[3] scripts below.
> >>>>
> >>>> [1]
> >>>> &cntrl
> >>>> imin=1,
> >>>> ntx=1,
> >>>> irest=0,
> >>>> ntpr=50,
> >>>> ntf=1,
> >>>> ntb=1,
> >>>> cut=9.0,
> >>>> nsnb=10,
> >>>> ntr=1,
> >>>> maxcyc=1000,
> >>>> ncyc=500,
> >>>> ntmin=1,
> >>>> restraintmask=':1-24',
> >>>> restraint_wt=25.0,
> >>>> &end
> >>>> &ewald
> >>>> ew_type = 0,
> >>>> skinnb = 1.0,
> >>>> &end
> >>>>
> >>>>
> >>>> [2]
> >>>> &cntrl
> >>>> imin=0,
> >>>> ntx=1,
> >>>> ntpr=500,
> >>>> ntwr=500,
> >>>> ntwx=500,
> >>>> ntwe=500,
> >>>> nscm=5000,
> >>>> ntf=2,
> >>>> ntc=2,
> >>>> ntb=1,
> >>>> ntp=0,
> >>>> nstlim=50000,
> >>>> t=0.0,
> >>>> dt=0.002,
> >>>> cut=9.0,
> >>>> tempi=100.0,
> >>>> ntt=1,
> >>>> ntr=1,
> >>>> nmropt=1,
> >>>> restraintmask=':1-24',
> >>>> restraint_wt=25.0,
> >>>> &end
> >>>> &wt
> >>>> type='TEMP0',
> >>>> istep1=0,
> >>>> istep2=5000,
> >>>> value1=100.0,
> >>>> value2=300.0,
> >>>> &end
> >>>> &wt
> >>>> type='TEMP0',
> >>>> istep1=5001,
> >>>> istep2=50000,
> >>>> value1=300.0,
> >>>> value2=300.0,
> >>>> &end
> >>>> &wt
> >>>> type='END',
> >>>> &end
> >>>>
> >>>>
> >>>> [3]
> >>>> &cntrl
> >>>> imin=0,
> >>>> ntx=5,
> >>>> ntpr=500,
> >>>> ntwr=500,
> >>>> ntwx=500,
> >>>> ntwe=500,
> >>>> nscm=5000,
> >>>> ntf=2,
> >>>> ntc=2,
> >>>> ntb=2,
> >>>> ntp=1,
> >>>> tautp=0.2,
> >>>> taup=0.2,
> >>>> nstlim=25000,
> >>>> t=0.0,
> >>>> dt=0.002,
> >>>> cut=9.0,
> >>>> ntt=1,
> >>>> ntr=1,
> >>>> irest=1,
> >>>> restraintmask=':1-24',
> >>>> restraint_wt=0.5,
> >>>> &end
> >>>> &ewald
> >>>> ew_type = 0,
> >>>> skinnb = 1.0,
> >>>> &end
> >>>>
> >>>>
> >>>> ——
> >>>> Jatin Kashyap
> >>>> Ph.D. Student
> >>>> Dr. Dibakar Datta Group
> >>>> Department of Mechanical and Industrial Engineering
> >>>> New Jersey Institute of Technology (NJIT)
> >>>> University Heights
> >>>> Newark, NJ 07102-1982
> >>>> Phone- (201)889-5783
> >>>> Email- jk435.njit.edu
> >>>>
> >>>>> On Jan 18, 2021, at 6:28 PM, Carlos Simmerling <
> >>>> carlos.simmerling.gmail.com> wrote:
> >>>>>
> >>>>> I can't find any text "mden" on that tutorial page. can you include
> the
> >>>>> actual job script for this so we can see where you defined it? mden
> >> might
> >>>>> be an energy output file, and maybe you don't have permission to
> write?
> >>>> but
> >>>>> we'll need to see the full script to know for sure.
> >>>>>
> >>>>> On Mon, Jan 18, 2021 at 6:17 PM Jatin Kashyap <jk435.njit.edu>
> wrote:
> >>>>>
> >>>>>> Dear AMBER Community,
> >>>>>>
> >>>>>> I am trying to reproduce the results of “Analysis of a nucleic acid
> >>>>>> simulation” tutorial.[1]
> >>>>>> I am facing a problem while running “eq.in” script as it's throwing
> >> an
> >>>>>> error[2] even before 1st step.
> >>>>>> I am using Amber 20 PMEMD 2020 on CPUs. All the scripts before this
> >> step
> >>>>>> i.e. mini.in & heat.in, are running fine.
> >>>>>>
> >>>>>> Can somebody please point-out where I am getting it wrong.
> >>>>>>
> >>>>>> Thank you.
> >>>>>>
> >>>>>> [1]
> >>>>>> https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/
> <
> >>>>>> https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/
> >
> >>>>>>
> >>>>>> [2]
> >>>>>> Nature and format of output:
> >>>>>> ntxo = 2, ntpr = 500, ntrx = 1, ntwr =
> >>>>>> 500
> >>>>>> iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
> >>>>>> 500
> >>>>>> ioutfm = 1, ntwprt = 0, idecomp = 0,
> rbornstat=
> >>>>>> 0
> >>>>>>
> >>>>>> Potential function:
> >>>>>> ntf = 2, ntb = 2, igb = 0, nsnb =
> >>>>>> 25
> >>>>>> ipol = 0, gbsa = 0, iesp = 0
> >>>>>> dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
> >>>>>>
> >>>>>> Frozen or restrained atoms:
> >>>>>> ibelly = 0, ntr = 1
> >>>>>> restraint_wt = 0.50000
> >>>>>>
> >>>>>> Molecular dynamics:
> >>>>>> nstlim = 25000, nscm = 0, nrespa = 1
> >>>>>> t = 0.00000, dt = 0.00200, vlimit = 20.00000
> >>>>>>
> >>>>>> Berendsen (weak-coupling) temperature regulation:
> >>>>>> temp0 = 300.00000, tempi = 0.00000, tautp = 0.20000
> >>>>>>
> >>>>>> Pressure regulation:
> >>>>>> ntp = 1
> >>>>>> pres0 = 1.00000, comp = 44.60000, taup = 0.20000
> >>>>>>
> >>>>>> SHAKE:
> >>>>>> ntc = 2, jfastw = 0
> >>>>>> tol = 0.00001
> >>>>>>
> >>>>>> | Intermolecular bonds treatment:
> >>>>>> | no_intermolecular_bonds = 1
> >>>>>>
> >>>>>> | Energy averages sample interval:
> >>>>>> | ene_avg_sampling = 500
> >>>>>>
> >>>>>> Extra-points options:
> >>>>>> frameon = 1, chngmask= 1
> >>>>>>
> >>>>>> Ewald parameters:
> >>>>>> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> >>>>>> 1
> >>>>>> vdwmeth = 1, eedmeth = 1, netfrc = 1
> >>>>>> Box X = 62.425 Box Y = 62.425 Box Z = 62.425
> >>>>>> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> >>>>>> NFFT1 = 64 NFFT2 = 64 NFFT3 = 64
> >>>>>> Cutoff= 9.000 Tol =0.100E-04
> >>>>>> Ewald Coefficient = 0.30768
> >>>>>> Interpolation order = 4
> >>>>>>
> >>>>>> LOADING THE CONSTRAINED ATOMS AS GROUPS
> >>>>>>
> >>>>>>
> >>>>>> 5. REFERENCE ATOM COORDINATES
> >>>>>>
> >>>>>> default_name
> >>>>>> Mask :1-24; matches 758 atoms
> >>>>>> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 15575 0
> >>>>>> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 15575 0
> >>>>>> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 5645 0
> >>>>>> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 544 0
> >>>>>> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 640 0
> >>>>>> | EXTRA_PTS, trim_theta: num angle AFTER trim = 640 0
> >>>>>> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 836 0
> >>>>>> | EXTRA_PTS, trim_theta: num angle AFTER trim = 836 0
> >>>>>> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1390 0
> >>>>>> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 1390 0
> >>>>>> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1756 0
> >>>>>> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 1756 0
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>
> --------------------------------------------------------------------------------
> >>>>>> 3. ATOMIC COORDINATES AND VELOCITIES
> >>>>>>
> >>>>>>
> >>>>
> >>
> --------------------------------------------------------------------------------
> >>>>>>
> >>>>>> default_name
> >>>>>> begin time read from input coords = 100.000 ps
> >>>>>>
> >>>>>>
> >>>>>> Unit 15 Error on OPEN: mden
> >>>>>>
> >>>>>> ——
> >>>>>> Jatin Kashyap
> >>>>>> Ph.D. Student
> >>>>>> Dr. Dibakar Datta Group
> >>>>>> Department of Mechanical and Industrial Engineering
> >>>>>> New Jersey Institute of Technology (NJIT)
> >>>>>> University Heights
> >>>>>> Newark, NJ 07102-1982
> >>>>>> Phone- (201)889-5783
> >>>>>> Email- jk435.njit.edu
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>
> >> _______________________________________________
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> >>
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Received on Mon Jan 18 2021 - 17:30:02 PST
