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

[Lara Bunte]

Hi Mark

Could you please give me for that the prompt how to write this in the console. 


"All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
  "Close to protein" resname LIG and within 0.5 of group "Protein" "


So how to put this into the console? I often found in the manual text that I don't know how to concretely type in into the bash console? 


Thanks for helping me and sorry for my questions. I am a noob :-(


Greetings
Lara





________________________________
 Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 11:51 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
 

On 13/04/2012 7:29 PM, Lara Bunte wrote: 
I read g_select -select 'help all' and I understand nothing of that. 
>
>
>
>In general one have a molecule (valences closed by hydrogen) and a water box around it. How to select only the protein with the first water layers, say one layer? 
>
>
>Please give me an example how to do this with gromacs. I read the examples in g_select -select 'help all' and I have no Idea what they are talking about. 
>
Surely you can see that the example

All atoms of a residue LIG within 0.5 nm of a protein (with a custom
    name):
  "Close to protein" resname LIG and within 0.5 of group "Protein" 

is very similar to what would be needed for all water residues
    within some distance of your solute.

VMD uses a similar approach. BioPython probably likewise. There's no
    genie going to wave the magic create-a-layer wand. You need to learn
    how to create a layer from a definition that suits you, because
    you'll probably have to vary that definition until you're happy with
    the outcome.

Mark



>
>Thanks for help
>Greetings
>Lara
>
>
>
> 
>
>
>
>________________________________
> Von: Mark Abraham <Mark.Abraham at anu.edu.au>
>An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Gesendet: 19:26 Mittwoch, 11.April 2012
>Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
> 
>On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>> 
>> 
>> Lara Bunte wrote:
>>> Could you please give how g_select is used?
>
>Reading g_select -h might have led you to try g_select
            -select 'help'
>
>>> Is there a tutorial for that?
>>> 
>> 
>> g_select -select 'help all'
>> 
>> The information contained therein is very extensive, so
            be sure to read it thoroughly.  It will fill several
            terminal windows explaining the syntax and providing
            examples.
>
>... and search Google for some examples.
>
>Mark
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