[gmx-users] MD simulations of two chains protein

tasneem kausar tasneemkausar12 at gmail.com
Tue Nov 15 08:11:08 CET 2016

Plot chain A and chain B separately. Residue no. in both the chain are
started from 1. It will overlap in same plot.

On Mon, Nov 14, 2016 at 5:03 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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