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

Lara Bunte lara.bunte at yahoo.de
Wed Apr 11 14:01:44 CEST 2012


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?


----- Ursprüngliche Message -----
Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
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.

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