[gmx-users] MD simulations of two chains protein

[Khadija Amine]

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*
>