Hi,
On Mon, Jan 4, 2021 at 3:57 AM Syeda Amna Arshi
<seyydaamnaarshi.gmail.com> wrote:
>
> The cpptraj command doesn't read the correct order of nc files for input,
Cpptraj follows standard filename wildcard rules. You need to either
change your naming scheme to use a fixed number of digits as
previously suggested, or change how you are using wildcards. For your
particular naming scheme, these are the wildcards I would use:
trajin md?.nc
trajin md??.nc
trajin md???.nc
trajin md????.nc
Hope this helps,
-Dan
PS - You can always check for yourself what order a particular
filename wildcard will result in by using something like "ls -l <name
with wildcards>".
> 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]
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Received on Mon Jan 04 2021 - 06:30:04 PST
