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

[Lara Bunte]

Hi

You are totally right. I am sorry. It is just so frustrating if you read the complete help more than once, understand nothing and than here all the time, that I should read the help. :-(

I like Gromacs and I am happy that it is free and I am very thankful for all the help here in the mailing list. 


But I also have to say (please don't take this an attack): If you are a total beginner and have no good knowledge about basic chemistry, it is really tough and frustrating reading the manual and help. There should be more help, especially how to type it in. Not everywhere but in the i.e. in the beginning of the manual a few words about that. 

I am from engineering and now I am in the physical chemistry. I want to learn! I am reading in the manual, the tutorials and in Chemistry for beginner books, but all the stuff is pretty hard if you are new in the topic....


About the topic:

Is there no way only to use the .pdb file? How do I create from a .pdb a rtp file. With pdb2gmx and than grompp?

Greetings
Lara






________________________________
 Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 15:40 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
 


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

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