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

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 13 14:59:38 CEST 2012

Lara Bunte wrote:
> Hi
> I tried but I got an error. In my mol_in_water.pdb file all atoms of my 
> molecule has the group notation ISO and all the water atoms has the 
> group notation SOL. I used following command:
> g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO" 
> resname SOL and within 0.5 of group "ISO"'
> and I got the error:
> Invalid command line argument:
> -other
> How can I fix it.

Please see g_select -h for valid options.  Mark was simply implying that you 
will likely need other command line options to make the program actually do 
something.  Also note the space in your "my mol_in_water.pdb" will cause 
problems as well.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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