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
>>>>
>>>> _______________________________________________
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>>>>
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Received on Mon Jan 18 2021 - 16:00:03 PST
