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

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 12 13:15:02 CEST 2008

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.


> Thanks in advance
> Sarbani
> Ebay 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null>
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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