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
>
> _______________________________________________
> 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
Received on Mon Jan 18 2021 - 16:30:02 PST
