[gmx-users] extract protein and counter ions from trajectory

[Justin A. Lemkul]

sarbani chattopadhyay wrote:
>  
> Hi everybody,
>                     I want to know is there any way to extract the 
> coordinates of both the protein and
> counterions from the trajectory while writing the "pdb" file ie. I don't 
> want the water molecules
> but only the protein and the counter ions.
> I did not see that option wile trying to generate the pdb files.
> 
> Is there any way of doing this?

As with every Gromacs analysis (and processing) tool, you can create an index 
file that contains whatever combination of groups you want.

-Justin

> 
> Thanks in advance
> 
> Sarbani
> 
> 
> 
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> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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