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

[Lara Bunte]

Thanks for that but where in this do I give Gromacs my pdb. file. From where do g_select use this information? 


What I have is a pdb file. 


Greetings
Lara





________________________________
 Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 12:06 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
 

On 13/04/2012 8:01 PM, Lara Bunte wrote: 
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 :-( 
>
The text for g_select -h in the upcoming GROMACS release will make
    this clearer, as others have struggled with this part recently.

g_select -other -options -select '"Close to protein" resname LIG and
    within 0.5 of group "Protein"'

works for that example. Note carefully the use of single and double
    quotes.

Mark



>
>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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>>
>
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