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

[francesco oteri]

Hi Lara, I sent an incomplete mail by error :(

I was saying that 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
    3. is the cutoff distance between protein and any other ATOM in the
system
3) "same residue" for each atom at point 2) it takes the corresponding
residue avoiding residue bracking.


If your pdb is more complex, but you need only water try:
"water and (same residue as within 3. of protein)".

Now you can visually inspect your selection and adjusting the distance.


When everything is fine, you can save it through vmd save comman:
1) in the command line write:

[atomselect top "same residue as within 3. of protein"] writepdb out.pdb

It should work and it should make the work easier!

Francesco







Il giorno 13 aprile 2012 11:38, francesco oteri
<francesco.oteri at gmail.com>ha scritto:

> 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 <lara.bunte at yahoo.de> 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 <Mark.Abraham at anu.edu.au>
>> *An:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> *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
>> -- gmx-users mailing list    gmx-users at gromacs.org
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>>
>>
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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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