Date: Tue, 5 Jan 2021 11:53:40 +0530
Hii,
thank you so much, the problem has been solved.
On Mon, Jan 4, 2021 at 2:26 PM Syeda Amna Arshi <seyydaamnaarshi.gmail.com>
wrote:
> The cpptraj command doesn't read the correct order of nc files for input,
> that command with wildcard read the .nc files as follows:
> md1000.nc
> md1001.nc
> md1002.nc
> md1003.nc
> md1004.nc
> md1005.nc
> md1006.nc
> md1007.nc
> md1008.nc
> md1009.nc
> md100.nc
> md1010.nc
> md1011.nc
> md1012.nc
> md1013.nc
> md1014.nc
> md1015.nc
> md1016.nc
> md1017.nc
> md1018.nc
> md1019.nc
> md101.nc and so on...
> please suggest the cpptraj command for *combining the 2500 nc files.*
>
> *thanks*
>
>
> On Thu, Dec 31, 2020 at 3:24 PM Syeda Amna Arshi <
> seyydaamnaarshi.gmail.com> wrote:
>
>> Hii,
>> first for combining the nc files i used following cpptraj input:
>> parm ABC_wation.prmtop
>> trajin md*.nc 1 last 10 # load frames in steps of 10
>> autoimage # automatic centre
>> strip :WAT # strip all residues with name WAT
>> trajout ABC_25.nc netcdf ! write out combined trajectory from 20.1ns run
>> go
>>
>>
>> further for the rmsd:
>> parm ABC_ion.prmtop
>> trajin ABC_25.nc
>> autoimage anchor :1-123
>> rms first out rmsd.dat .CA
>>
>> and the resultant plot is attached below
>>
>>
>> [image: image.png]
>>
>> On Thu, Dec 24, 2020 at 12:02 PM Syeda Amna Arshi <
>> seyydaamnaarshi.gmail.com> wrote:
>>
>>> I am very confused after autoimage it shows same drops in the rmsd at
>>> the same time point. Please look at the input files also may be i have to
>>> change the parameters.
>>>
>>> On Mon, Dec 21, 2020 at 12:39 PM Syeda Amna Arshi <
>>> seyydaamnaarshi.gmail.com> wrote:
>>>
>>>> I think that my complex has been moving out of the octahedron water box
>>>> (TIP3PBOX) during the simulation, it looks like part of the complex goes
>>>> out of the box at many points. Are there any parameters in my input files
>>>> that I should try adjusting?
>>>> Here are the settings that I used for my input files
>>>>
>>>> --complex initial minimization solvent + ions
>>>> &cntrl imin = 1,maxcyc = 3000,ncyc = 1500,ntb = 1,ntr =
>>>> 1,cut = 10.0/
>>>> Hold the Protein + DNA fixed
>>>> 100.0
>>>> RES 1 153
>>>> END
>>>> END
>>>>
>>>> --complex initial minimization solvent + ions
>>>> &cntrl imin = 1,maxcyc = 5000,ncyc = 2500,ntb = 1,ntr =
>>>> 1,cut = 10.0/
>>>> Hold the Protein + DNA fixed
>>>> 25.0
>>>> RES 1 153
>>>> END
>>>> END
>>>>
>>>> --Complex minimization for whole system without restraint
>>>> &cntrl imin = 1,maxcyc = 5000,ncyc = 2500,ntb = 1,ntr =
>>>> 0,cut = 10.0/
>>>>
>>>>
>>>> --complex: 20ps MD with res on the protein + DNA complex
>>>> &cntrl
>>>> imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10.0,
>>>> ntr = 1, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0,ntt
>>>> = 3, gamma_ln = 1.0, nstlim = 10000, dt = 0.002, ntpr = 10000, ntwx =
>>>> 10000, ntwr = 10000,
>>>>
>>>> /
>>>> Keep DNA fixed with weak restraints
>>>> 10.0
>>>> RES 1 153
>>>> END
>>>> END
>>>>
>>>>
>>>> --complex: 80ps MD with 0.5 Kcal res on protein + DNA complex
>>>> &cntrl
>>>> imin = 0, irest = 1, ntx = 7, ntb = 1, cut = 10.0,
>>>> ntr = 1, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0,
>>>> ntt = 3, gamma_ln = 1.0, nstlim = 40000, dt = 0.002, ntpr =
>>>> 40000, ntwx = 40000, ntwr = 40000 ig = -1
>>>> /
>>>> Keep Protein + DNA fixed with weak restraints
>>>> 0.5
>>>> RES 1 153
>>>> END
>>>> END
>>>>
>>>>
>>>>
>>>> --complex: 200ps of MD
>>>> &cntrl
>>>> imin = 0, irest = 1, ntx = 7,
>>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>>> taup = 2.0,
>>>> cut = 10.0, ntr = 0, ig = -1,
>>>> ntc = 2, ntf = 2,
>>>> tempi = 300.0, temp0 = 300.0,
>>>> ntt = 3, gamma_ln = 1.0,
>>>> nstlim = 100000, dt = 0.002,
>>>> ntpr = 100000, ntwx = 10000, ntwr = 100000
>>>> /
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Sincerely,
>>>>
>>>> *Syeda Amna Arshi*
>>>>
>>>> *Ph.D. Scholar*
>>>>
>>>> Multidisciplinary Centre For Advanced Research and Studies
>>>>
>>>> Jamia Millia Islamia
>>>>
>>>> Delhi-110025
>>>>
>>>> Ph.no: 7737638065
>>>>
>>>>
>>>> [image: Image result for save world by plant][image: Image result for
>>>> save world by plant white background]
>>>>
>>>
>>>
>>> --
>>>
>>> Sincerely,
>>>
>>> *Syeda Amna Arshi*
>>>
>>> *Ph.D. Scholar*
>>>
>>> Multidisciplinary Centre For Advanced Research and Studies
>>>
>>> Jamia Millia Islamia
>>>
>>> Delhi-110025
>>>
>>> Ph.no: 7737638065
>>>
>>>
>>> [image: Image result for save world by plant][image: Image result for
>>> save world by plant white background]
>>>
>>
>>
>> --
>>
>> Sincerely,
>>
>> *Syeda Amna Arshi*
>>
>> *Ph.D. Scholar*
>>
>> Multidisciplinary Centre For Advanced Research and Studies
>>
>> Jamia Millia Islamia
>>
>> Delhi-110025
>>
>> Ph.no: 7737638065
>>
>>
>> [image: Image result for save world by plant][image: Image result for
>> save world by plant white background]
>>
>
>
> --
>
> Sincerely,
>
> *Syeda Amna Arshi*
>
> *Ph.D. Scholar*
>
> Multidisciplinary Centre For Advanced Research and Studies
>
> Jamia Millia Islamia
>
> Delhi-110025
>
> Ph.no: 7737638065
>
>
> [image: Image result for save world by plant][image: Image result for
> save world by plant white background]
>
-- Sincerely, *Syeda Amna Arshi* *Ph.D. Scholar* Multidisciplinary Centre For Advanced Research and Studies Jamia Millia Islamia Delhi-110025 Ph.no: 7737638065 [image: Image result for save world by plant][image: Image result for save world by plant white background]
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