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

Lara Bunte lara.bunte at yahoo.de
Sat Apr 14 16:42:13 CEST 2012

I still got the problem. What is wrong in this command:

g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'

In the pdb. file ISO is for the molecule and SOL for the water.

Please help


 Von: Teemu Murtola <teemu.murtola at cbr.su.se>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 18:20 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
On Fri, Apr 13, 2012 at 18:30, Lara Bunte <lara.bunte at yahoo.de> wrote:
> Is there no way only to use the .pdb file? How do I create from a .pdb a rtp
> file. With pdb2gmx and than grompp?

You can also provide a .pdb file to the -s option of g_select. And you
don't need to provide a -f file in that case if you simply want to
analyze the coordinates in a single configuration of that .pdb file.

Best regards,
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