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

[Lara Bunte]

Hi Justin

Okay, after 


g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'


I got:

selection parser: invalid selection '"Close to ISO" resname SOL and within 0.5 of group "ISO"'

Input error or input inconsistency:
selection(s) could not be parsed


I also tried other permutations of ISO and SOL and got the same. 


I read the complete help to g_select twice and I understand nothing what there is written.  In general I like Gromacs more and more but g_select program is totally fucked. I don't get it. :-(

Greetings
Lara

p.s.
Here in this email if I got to answer (like always) is only Justins mail adress, not the gromacs user list. I do it in cc







________________________________
 Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 14:59 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
 


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

-- ========================================

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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