[gmx-users] trjconv index file

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 16 13:26:31 CEST 2010

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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