[gmx-users] File editing - only one layer of water around a molecule

[Justin A. Lemkul]

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 <jalemkul at vt.edu>
> *An:* Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS 
> users <gmx-users at 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

========================================