[gmx-users] MD simulations of two chains protein

[tasneem kausar]

I have suggested you in previous mail to plot chain A and chain B
separately. I have looked at the link. It is because of the same residue
number in chain A and chain B. In xvg file chain identifier (A/B) will not
be shown. Just open .xvg file in any text editor. Copy the residue number
and their corresponding rmsd values of chain A. Paste it in orgin software
or excel and plot. Do the same for chain B residues.
  Make_ndx option of gromacs can also help you. Make index file for chain A
and chain B. Calculate RMSF of chain A and then RMSF of chain B.
Hope this will help you.


On Thu, Nov 17, 2016 at 1:07 PM, Khadija Amine <kh.amine1 at gmail.com> wrote:

> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Wed, Nov 16, 2016 at 9:15 AM, Khadija Amine <kh.amine1 at gmail.com>
> wrote:
>
> > Hi Mark,
> >
> > Below, the link to the rmsf plot I had for my protein throughout 20 ns
> > simulation.
> >
> > https://www.dropbox.com/s/v67u8iplcyl506q/rmsfmergemut.png?dl=0
> >
> > The command I used is: gmx rmsf -s XXX.tpr -f XXX.xtc -o rmsf.xvg -oq
> > rmsf.pdb -res
> >
> > Thank you
> >
> > *Khadija AMINE*
> >
> >
> > *Computational Biology*
> > *Postdoctoral Research Associate*
> > *Carnegie Mellon University*
> >
> > On Tue, Nov 15, 2016 at 10:50 AM, Khadija Amine <kh.amine1 at gmail.com>
> > wrote:
> >
> >> Ok I will try that.
> >>
> >> There is a way to specify the regions to plot in RMSF using rms tool?
> >>
> >> Thank you
> >>
> >> *Khadija AMINE*
> >>
> >>
> >> *Computational Biology*
> >> *Postdoctoral Research Associate*
> >> *Carnegie Mellon University*
> >>
> >> On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine <kh.amine1 at gmail.com>
> >> wrote:
> >>
> >>> Hello,
> >>>
> >>> Can someone show me how can I proceed?
> >>>
> >>> Thank you
> >>>
> >>> *Khadija AMINE*
> >>>
> >>>
> >>> *Computational Biology*
> >>> *Postdoctoral Research Associate*
> >>> *Carnegie Mellon University*
> >>>
> >>> On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine <kh.amine1 at gmail.com>
> >>> wrote:
> >>>
> >>>> Dear Gromacs users,
> >>>>
> >>>> I need your help regarding MD simulation of two chains protein.
> >>>> The chain A is 2-78 aa, and the chain B is 1-168 aa.
> >>>>
> >>>> I started with the pdb file where there is specified names of the two
> >>>> chains as A and B.
> >>>>
> >>>> I did solvation of my system in a cubic box, I tried to open the
> >>>> pdb file issued from this step I didn't find the column specifying the
> >>>> chain names.
> >>>>
> >>>> I run 20 ns of MD for this protein. The RMSF plot of the protein seems
> >>>> to be overlapping from 1 to 78 and the rest of the residues flctuation
> >>>> is good.
> >>>>
> >>>> As it is the first time am facing such issues with protein with two
> >>>> chains, how can I avoid such overlap in RMSF plot?
> >>>>
> >>>> Is this linked to the chains numbering issued after writing the
> >>>> topology.
> >>>>
> >>>> Thank you
> >>>>
> >>>> *Khadija AMINE*
> >>>>
> >>>>
> >>>> *Computational Biology*
> >>>> *Postdoctoral Research Associate*
> >>>> *Carnegie Mellon University*
> >>>>
> >>>
> >>>
> >>
> >
> --
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