Could you please give how g_select is used?
Is there a tutorial for that?
Greetings
Lara
________________________________
Von: Mark Abraham <mark.abra...@anu.edu.au>
An: Discussion list for GROMACS users <gmx-users@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.abra...@anu.edu.au>
>An: Lara Bunte <lara.bu...@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.bu...@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.abra...@anu.edu.au>
>>An: Discussion list for GROMACS users <gmx-users@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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