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

[Lara Bunte]

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? 


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? 


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?

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

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