Hi Lara,
the simplest way is using vmd.
Briefly,
1) load the pdb file in vmd.
2) create a representation using a string like: "same residue as within 3.
of protein".
where "protein" is the group around the molecule you have to use, I
used protein just as example
Il giorno 13 aprile 2012 11:29, Lara Bunte <[email protected]> ha scritto:
> I read g_select -select 'help all' and I understand nothing of that.
>
> In general one have a molecule (valences closed by hydrogen) and a water
> box around it. How to select only the protein with the first water layers,
> say one layer?
>
> Please give me an example how to do this with gromacs. I read the examples
> in g_select -select 'help all' and I have no Idea what they are talking
> about.
>
> Thanks for help
> Greetings
> Lara
>
>
>
> ------------------------------
> *Von:* Mark Abraham <[email protected]>
> *An:* Discussion list for GROMACS users <[email protected]>
> *Gesendet:* 19:26 Mittwoch, 11.April 2012
>
> *Betreff:* Re: [gmx-users] File editing - only one layer of water around
> a molecule
>
> On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
> >
> >
> > Lara Bunte wrote:
> >> Could you please give how g_select is used?
>
> Reading g_select -h might have led you to try g_select -select 'help'
>
> >> Is there a tutorial for that?
> >>
> >
> > g_select -select 'help all'
> >
> > The information contained therein is very extensive, so be sure to read
> it thoroughly. It will fill several terminal windows explaining the syntax
> and providing examples.
>
> ... and search Google for some examples.
>
> Mark
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--
Cordiali saluti, Dr.Oteri Francesco
--
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