Hi Justin
Okay, after
g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5
of group "ISO"'
I got:
selection parser: invalid selection '"Close to ISO" resname SOL and within 0.5
of group "ISO"'
Input error or input inconsistency:
selection(s) could not be parsed
I also tried other permutations of ISO and SOL and got the same.
I read the complete help to g_select twice and I understand nothing what there
is written. In general I like Gromacs more and more but g_select program is
totally fucked. I don't get it. :-(
Greetings
Lara
p.s.
Here in this email if I got to answer (like always) is only Justins mail
adress, not the gromacs user list. I do it in cc
________________________________
Von: Justin A. Lemkul <jalem...@vt.edu>
An: Lara Bunte <lara.bu...@yahoo.de>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Gesendet: 14:59 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
Lara Bunte wrote:
> Hi
>
> I tried but I got an error. In my mol_in_water.pdb file all atoms of my
> molecule has the group notation ISO and all the water atoms has the group
> notation SOL. I used following command:
>
> g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO"
> resname SOL and within 0.5 of group "ISO"'
>
> and I got the error:
>
> Invalid command line argument:
> -other
>
> How can I fix it.
>
Please see g_select -h for valid options. Mark was simply implying that you
will likely need other command line options to make the program actually do
something. Also note the space in your "my mol_in_water.pdb" will cause
problems as well.
-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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