[gmx-users] trjconv index file

Rabab Toubar rtoubar at yahoo.com
Wed Jun 16 13:10:29 CEST 2010


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 

Am I missing something?
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


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