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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