Lara Bunte wrote:
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. :-(
There is absolutely no need for crude language. We all understand frustration,
but insulting someone else's work, especially in this manner, is unprofessional
and uncalled for. The development of g_select required a heroic amount of
effort. It is a complicated program, to be sure, and the documentation is
improving (as is true for all Gromacs programs, to differing extents). How much
did you pay for Gromacs? How much do you pay for technical support? Keep that
in mind. I'm not easily offended, but the other several thousand users of this
list might become highly unlikely to help a hothead who could curse them out if
the proper answer isn't received.
Provide a .tpr file to the -s flag of g_select; it should solve the problem.
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
Configure your mail client to reply-all by default or replace the address.
-Justin
------------------------------------------------------------------------
*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
========================================
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
