[gmx-users] MD simulations of two chains protein

[Khadija Amine]

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*
>>
>
>