That looks ok if you are the owner.
On Mon, Jan 18, 2021, 8:40 PM Jatin Kashyap <jk435.njit.edu> wrote:
> It is showing below:
>
> -rw-r--r-- 1 Jan 18 17:26 mden
>
> 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 8:12 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
> >
> > 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
> >>>>
> >>>> _______________________________________________
> >>>> 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 - 18:30:02 PST
