[gmx-users] trjconv index file

[Rabab Toubar]

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

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
-------------------------------------------------------
$ 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
-------------------------------------------------------

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
-------------------------------------------------------



> -Justin
> 
> > Thanks
> > Rabab Toubar
> > 
> > 
> > --- On Tue, 6/15/10, Mark Abraham <mark.abraham at anu.edu.au>
> wrote:
> > 
> > From: Mark Abraham <mark.abraham at anu.edu.au>
> > Subject: Re: [gmx-users] trjconv index file
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Date: Tuesday, June 15, 2010, 6:10 PM
> > 
> > 
> > 
> > ----- Original Message -----
> > From: Rabab Toubar <rtoubar at yahoo.com>
> > Date: Wednesday, June 16, 2010 1:44
> > Subject: [gmx-users] trjconv index file
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > 
> >> Trying to extract the protein from the md run
> without waters, all the mailing lists suggests using an
> index file
> >>  before running trjconv, but I get file
> input/output error
> >>  Can someone give me more details on how to
> egt the index
> >>  file
> > 
> > If you want useful help, you have to tell us exactly
> what you did - copy and paste command lines and output.
> > 
> > Otherwise, you'll just get people throwing up their
> hands and giving you a reference to generic material, like
> http://www.gromacs.org/Documentation/File_Formats/Index_File
> > 
> > Mark
> > 
> > -----Inline Attachment Follows-----
> > 
> 
> -- ========================================
> 
> 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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