Hi,
three short remarks:
a, Make sure that your use of the wildcard * in the trajin command
creates the correct order of your nc files for input and does not read
in any unwanted files as well (ls -1 md*.nc)
b, You may want to call the strip-command before the autoimage command,
because you do not need to reimage the water molecules, if you discard
them later (should speed up your analysis).
c, Your atom mask in the rms command is wrong: Use .CA to denote all
carbon alpha atoms of your protein (or .C,CA,N for the protein backbone).
How does your protein RMSD plot look then?
Regards,
Anselm
Am 31.12.2020 um 10:54 schrieb Syeda Amna Arshi:
> 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]
>>
>
>
>
>
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Received on Thu Dec 31 2020 - 02:30:02 PST
