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

Lara Bunte lara.bunte at yahoo.de
Tue May 1 20:40:55 CEST 2012


There is a new problem :-(

If I used the commands

g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within 1.2 of resname ISO'


trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb

I got only water in my output.pdb

Than I tried all 8 possible permutations of ISO and SOL in g_select and I always got only water or only the molecule without any water. 

But what I need is the molecule and only three layers of water around the molecule. 

What is the problem? 

Thanks for helping me.


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