[gmx-users] File editing - only one layer of water around a molecule

[Justin A. Lemkul]

Lara Bunte wrote:
> I still got the problem. What is wrong in this command:
> 
> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL 
> and within 0.5 of group "ISO"'
> 
> In the pdb. file ISO is for the molecule and SOL for the water.
> 
> Please help
> 

The above command assumes "ISO" is a default group, like "Protein" or something 
else.  You can make selections based on any arbitrary residue name with 
something like the following:

g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 
0.5 of resname ISO'

Does that work?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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