Rabab Toubar wrote:
Rabab Toubar
--- On Wed, 6/16/10, Justin A. Lemkul <[email protected]> wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] trjconv index file
To: "Discussion list for GROMACS users" <[email protected]>
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
========================================
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