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

Sun Apr 22 21:55:44 CEST 2012

Hi Justin

You wrote: 

>If you do not specify any output file, the default is this .xvg file 
that tells you how many atoms satisfied the >criterion specified in the 
selection string. If you want a coordinate file, it's a two-step 
process.
>
>1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion.
>
>2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms.
I used the command:

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

And got the size.xvg file and an index.ndx file. Than I want to make my coordinate file by

trjconv -n index.ndx

and got the error

Can not open file:
traj.xtc

I have no traj.xtc file. 

Thank you for helping me

Greetings
Lara

________________________________
 Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 17:27 Samstag, 14.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule

Lara Bunte wrote:
> Hi Justin
> 
> The difference in my
> 
> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of group "ISO"'
> 
> and your
> 
> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO'
> 
> is, that the last ISO is not in quotation marks. Could you please explain?
> 

There is a much greater difference.  The first command uses 'group "ISO"' which assumes that there is a group (either generated by default or present in a supplied index file) named "ISO."  Apparently this is not the case.  What I used was 'resname ISO' which is generic syntax for any residue name that I like (i.e., not a group).  You can use it with any residue name in the structure.

> With your command I got this time no error but I got other stuff that I don't understand:
> 
> 1.)
> I got this warnings:
> 
> WARNING: masses and atomic (Van der Waals) radii will be determined
>          based on residue and atom names. These numbers can deviate
>          from the correct mass and radius of the atom type.
> 
> 
> WARNING: if there are broken molecules in the trajectory file,
>          they can not be made whole without a run input file
> 
> Can I ignore this or is this serious?
> 

These are probably not important.  They are generic warnings that many Gromacs programs will produce if they are run without a .tpr file.

> 2.)
> My output is one file called size.xvg. It contains
> 
> # This file was created Sat Apr 14 16:55:56 2012
> # by the following command:
> # g_select -s molecule_in_water.pdb -select "Close to ISO" resname SOL and within 0.5 of resname ISO
> #
> # g_select is part of G R O M A C S:
> #
> # Green Red Orange Magenta Azure Cyan Skyblue
> #
> @    title "Selection size"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Number"
> @TYPE xy
> # Selections:
> #   "Close to ISO" resname SOL and within 0.5 of resname ISO
> #
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Close to ISO"
>       0.000  848.000
> 
> What is the interpretation of this? What I need is a new pdb. file that has to contain only the molecule ISO and the water layer SOL around it. Is this possible with g_select?
> 

If you do not specify any output file, the default is this .xvg file that tells you how many atoms satisfied the criterion specified in the selection string. If you want a coordinate file, it's a two-step process.

1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion.

2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms.

-Justin

> Thanks for helping me.
> Greetings
> Lara
> 
> 
> p.s.
> I use yahoo. I tried to find an "answer to all" option or something like that. Again after pressing answer the mail should go only to Justin. I put the mailing list in cc. Is here someone using yahoo also and know how to fix this?
> 
> 
> 
> 
> ------------------------------------------------------------------------
> *Von:* Justin A. Lemkul <jalemkul at vt.edu>
> *An:* Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Gesendet:* 16:56 Samstag, 14.April 2012
> *Betreff:* Re: [gmx-users] File editing - only one layer of water around a molecule
> 
> 
> 
> Lara Bunte wrote:
>  > 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
>  >
> 
> The above command assumes "ISO" is a default group, like "Protein" or something else.  You can make selections based on any arbitrary residue name with something like the following:
> 
> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO'
> 
> Does that work?
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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