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

[Mark Abraham]

On 13/04/2012 8:17 PM, Lara Bunte wrote:
> 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.

Look at g_select -h for -f and -s. Like every GROMACS tool, .pdb is one 
of the file types you can use instead of a trajectory or run input file 
in cases where (as here) that makes sense.

On a more general note, I hope you've done all the GROMACS tutorial 
material you can find - this question is one example of the kind of 
usage "general knowledge" that can often be acquired that way.

Mark

>
> 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> 
>> <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:* 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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>
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