[gmx-users] MD simulations of two chains protein

[Khadija Amine]

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*
>>>
>>
>>
>