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

[Lara Bunte]

Could you please give how g_select is used?
Is there a tutorial for that?

Greetings
Lara




________________________________
 Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 15:57 Mittwoch, 11.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
 

Please leave the discussion on the mailing list, so that others can contribute and benefit now and via the archives.

On 11/04/2012 10:53 PM, Lara Bunte wrote: 
Hi
>
>
>How to do that? I searched the manual for "layer" and I don't find something that helped. I also have no idea about what distances.
There's no standard definition of a layer - it depends what you're
    trying to do. A layer around a protein with a concavity might need
    to be defined quite differently from a layer around a monatomic ion
    or next to a hydrophobic phase boundary.

Ultimately, you need to get some idea about distances :-) Look up
    how long a water O-H bond is. Wikipedia will do. What does your
    knowledge of the structure of water suggest about a likely range for
    a O-H-O distance? How does that relate to how big a "layer" might
    be? Do you care how rough the layer is? Do you care if your layer
    has water molecule(s) between a water molecule and your solute? Use
    g_select to select water atoms within some range of your solute and
    look at the results.

Mark


I have a small molecule in a big water box and I only want one layer (later 2, 3, ..n) that I want to keep around the molecule and remove the rest. 
>
>
>
>In appendix I put one of this .pdb files that you can see what I mean. 
>
>
>
>Thanks for help
>
>
>Greetings
>Lara
>
>
>
>
>
>
>________________________________
> Von: Mark Abraham <mark.abraham at anu.edu.au>
>An: Lara Bunte <lara.bunte at yahoo.de> 
>Gesendet: 14:07 Mittwoch, 11.April 2012
>Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
> 
>
> 
> On 11/04/12, Lara Bunte <lara.bunte at yahoo.de> wrote: 
>Hi
>>
>>I read g_select description and I still don't know how
                to solve my problem. No if you have a pdb file with a
                molecule in water. How to remove all the water except of
                one layer? How could I do this with g_select? What other
                solutions could be used, with i.e. other software?
> 
>First, define "a layer" in a way that suits what you are trying to observe. Copy literature approaches if suitable. Then seek to cast that definition in terms of distances between atoms, which is all that you have to work with.
> 
>Mark 
> 
>
>>
>>Greetings
>>Lara
>>
>>
>>
>>
>>
>>
>>----- Ursprüngliche Message -----
>>Von: Mark Abraham <Mark.Abraham at anu.edu.au>
>>An: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>CC: 
>>Gesendet: 14:27 Mittwoch, 4.April 2012
>>Betreff: Re: [gmx-users] File editing - only one layer
                  of water around a molecule
>>
>>On 4/04/2012 7:27 PM, Lara Bunte wrote:
>>> Hello
>>> 
>>> I have a question about editing a pdb file.
>>> 
>>> I have a molecule in a box of water as a pdb
                  file. I want to remove all water except of ONE layer
                  around he molecule.  How to do that?
>>> 
>>> 
>>> Do you know a software that is able to do that?
                  Do you know how it could work with programs like PyMol
                  or others?
>>
>>There's many ways to do it. The GROMACS way is to use
                  g_select with some geometric criterion for the layer
                  to generate an index group describing the layer, and
                  then using that with trjconv -n to take the subset out
                  of the trajectory file.
>>
>>Mark
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> 
>
>

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