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
>>>>>>>>
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Received on Mon Jan 18 2021 - 18:00:02 PST
