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 <jalem...@vt.edu>
An: Lara Bunte <lara.bu...@yahoo.de>; Discussion list for GROMACS users
<gmx-users@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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