Date: Thu, 31 Dec 2020 15:24:41 +0530
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]
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(image/png attachment: image.png)
