[gmx-users] MD simulations of two chains protein

[Khadija Amine]

*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*
>>>>
>>>
>>>
>>
>