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.
-Justin
Thanks
Rabab Toubar
--- On Tue, 6/15/10, Mark Abraham <mark.abra...@anu.edu.au> wrote:
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] trjconv index file
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Tuesday, June 15, 2010, 6:10 PM
----- Original Message -----
From: Rabab Toubar <rtou...@yahoo.com>
Date: Wednesday, June 16, 2010 1:44
Subject: [gmx-users] trjconv index file
To: Discussion list for GROMACS users <gmx-users@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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