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

[Mark Abraham]

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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