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 - 16:30:02 PST
