On 15/04/2012 1:15 AM, 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?
The significant difference is that you refer to "group "ISO"" without
defining that group (since it is not defined by default, unlike the
example group named Protein), and Justin refers to the RESidue NAMEd
"ISO" with "resname ISO".
As you would know if you had more experience with the Unix command line,
quotation marks are sometimes necessary to help delineate what groups of
words make sense where (e.g. in English
Mark said "Justin said do this"
differs from
"Mark said," Justin said, "do this"). Sometimes you can get away with no
quotation marks around something if the purpose of the quotation marks
is merely grouping and the thing is only one word long. So the selection
string needs quotation marks around "Close to ISO" to group those words
to create a new index group with that name, the command line needs
quotation marks around the selection string to group all those words,
but Justin's resname might/can survive without. Unlike a reader of the
written word, the UNIX shell parser is not endowed with higher
intellect, so one needs to use different quotation marks to handle
nesting, or explicitly delineate the nesting... but that is a topic you
can Google about at your leisure.
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.
Unlike programs that just guess stuff and don't ever tell you about it
(which explains 99% of the posts on this list about the behaviour of
VMD), GROMACS warns you that it's going to have to make guesses about
your input since it comes in .pdb form. Input in .tpr form would allow
the tool to make definitive assignments. If you had an atom named "HG"
that was intended to be mercury or a hydrogen on a gamma carbon, you
should go check the results made sense. So you should judge for yourself
how weird your atom names are with respect to standard PDB naming, and
whether you even use the masses or VDW radii in your calculation.
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?
I've now improved this error message in the code. Molecules can be
"broken" across periodic boundaries under some circumstances. Since
you're using .pdb input, and GROMACS tools make no attempt to use the
PDB format for atomic connectivity even if it is present, GROMACS is
warning you that you need to consider this aspect yourself. Inspecting
the relevant coordinates in the file or a visualization program and
comparing them with the location of the periodic box might be necessary,
depending how your input file was created. You will normally know things
about your files that GROMACS cannot know.
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?
No. g_select has defaulted silently to the behaviour for g_select -os,
which you can read about in g_select -h. That's no good to you, of
course. You need an index group that you can use with another tool (e.g.
trjconv) to actually make the selection. (Future GROMACS versions will
be able to do this in one step, but that nirvana yet awaits.) For the
exercise, please look up the correct output option for this from
g_select -h.
Mark
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 <[email protected]>
*An:* Lara Bunte <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*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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