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

[Mark Abraham]

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> 
>> <mailto:Mark.Abraham at anu.edu.au>
>> *An:* Discussion list for GROMACS users <gmx-users at gromacs.org> 
>> <mailto: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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