[gmx-users] trjconv index file

[Justin A. Lemkul]

Rabab Toubar wrote:
> Rabab Toubar
> 
> 
> 
> --- On Wed, 6/16/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 
>> From: Justin A. Lemkul <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] trjconv index file
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Date: Wednesday, June 16, 2010, 7:26 AM
>>
>>
>> Rabab Toubar wrote:
>>> Hi,
>>>
>>> I want to extract the protein only without the waters.
>> And from the mailing list discussing trjconv, what I did
>> was:
>>> make_ndx -f conf-protein 
>>> trajconv -f pr.trr -n index.ndx -o pr_trj.trr
>>>
>>> , but I get file input/output error 
>> The *actual* error message would be substantially more
>> useful.  Without it, we don't know which file trjconv
>> is complaining about.  Also, please copy and paste your
>> commands from the terminal instead of trying to replicate
>> what you think you typed.  Your problem could be
>> something as simple as a typo (like "trajconv").
>>
>>> Am I missing something?
>> As I said before, default groups need not be re-created in
>> an index file.  You should simply be able to dump out
>> the protein coordinates from trjconv directly with no
>> special intervention.
>>
> 
> How can I possibly do that, I looked into the manual and the mailing list and all what I could find is what I tried..If there is an easier way to extract just the protein from the whole system, please let me know
> 

Have you actually tried it?  The following command does exactly what you want 
(assuming every filename is prefixed with "pr"):

trjconv -s pr.tpr -f pr.trr

Choose "Protein" for output.

> below is what I did copied from the terminal:
> $ make_ndx -f conf-protein
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>               GROningen Mixture of Alchemy and Childrens' Stories
> 
>                             :-)  VERSION 3.3.3  (-:
> 
> 
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, The GROMACS development team,
>             check out http://www.gromacs.org for more information.
> 
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
> 
>                                :-)  make_ndx  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f conf-protein.gro  Input, Opt!  Generic structure: gro g96 pdb tpr tpb
>                                    tpa xml
>   -n      index.ndx  Input, Opt., Mult. Index file
>   -o      index.ndx  Output       Index file
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -natoms      int    0       set number of atoms (default: read from
>                             coordinate or index file)
> 
> 
> -------------------------------------------------------
> Program make_ndx, VERSION 3.3.3
> Source code file: futil.c, line: 345
> 
> File input/output error:
> conf-protein.gro
> -------------------------------------------------------

If make_ndx fails, then nothing else relying on the index file will work.  It 
looks like you don't have a file named "conf-protein.gro" in the working directory.

> $ trjconv -f pr.trr -n conf-protein.ndx -o pr_new.trr
> -------------------------------------------------------
> Program trjconv, VERSION 3.3.3
> Source code file: futil.c, line: 345
> 
> File input/output error:
> conf-protein.ndx
> -------------------------------------------------------
> 

The default output of make_ndx is "index.ndx," but since make_ndx failed, 
there's certainly no index file for you to use.

> I also tried:
> $ trjconv -f pr.trr -n index.ndx -o pr_new.trr
> -------------------------------------------------------
> Program trjconv, VERSION 3.3.3
> Source code file: futil.c, line: 345
> 
> File input/output error:
> index.ndx
> -------------------------------------------------------
> 

Right, because make_ndx failed from not finding your coordinate file.  Check the 
contents of your working directory with ls to see what's actually there.

-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

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