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 <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
========================================
--
========================================
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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