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

Lara Bunte lara.bunte at yahoo.de
Fri Apr 13 14:56:40 CEST 2012 

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.


Greetings
Lara






________________________________
 Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 12:23 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
 

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>
>>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
>>>-- gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>
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