On 13/04/2012 8:17 PM, Lara Bunte wrote:
Thanks for that but where in this do I give Gromacs my pdb. file. From
where do g_select use this information?
What I have is a pdb file.
Look at g_select -h for -f and -s. Like every GROMACS tool, .pdb is one
of the file types you can use instead of a trajectory or run input file
in cases where (as here) that makes sense.
On a more general note, I hope you've done all the GROMACS tutorial
material you can find - this question is one example of the kind of
usage "general knowledge" that can often be acquired that way.
Mark
Greetings
Lara
------------------------------------------------------------------------
*Von:* Mark Abraham <mark.abra...@anu.edu.au>
*An:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Gesendet:* 12:06 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water
around a molecule
On 13/04/2012 8:01 PM, Lara Bunte wrote:
Hi Mark
Could you please give me for that the prompt how to write this in the
console.
"All atoms of a residue LIG within 0.5 nm of a protein (with a custom
name):
"Close to protein" resname LIG and within 0.5 of group "Protein" "
So how to put this into the console? I often found in the manual text
that I don't know how to concretely type in into the bash console?
Thanks for helping me and sorry for my questions. I am a noob :-(
The text for g_select -h in the upcoming GROMACS release will make
this clearer, as others have struggled with this part recently.
g_select -other -options -select '"Close to protein" resname LIG and
within 0.5 of group "Protein"'
works for that example. Note carefully the use of single and double
quotes.
Mark
Greetings
Lara
------------------------------------------------------------------------
*Von:* Mark Abraham <mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au>
*An:* Discussion list for GROMACS users <gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org>
*Gesendet:* 11:51 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water
around a molecule
On 13/04/2012 7:29 PM, Lara Bunte wrote:
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.
Surely you can see that the example
All atoms of a residue LIG within 0.5 nm of a protein (with a custom
name):
"Close to protein" resname LIG and within 0.5 of group "Protein"
is very similar to what would be needed for all water residues within
some distance of your solute.
VMD uses a similar approach. BioPython probably likewise. There's no
genie going to wave the magic create-a-layer wand. You need to learn
how to create a layer from a definition that suits you, because
you'll probably have to vary that definition until you're happy with
the outcome.
Mark
Thanks for help
Greetings
Lara
------------------------------------------------------------------------
*Von:* Mark Abraham <mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au>
*An:* Discussion list for GROMACS users <gmx-users@gromacs.org>
<mailto:gmx-users@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@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
