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 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 <[email protected]> > wrote: > > > > From: Mark Abraham <[email protected]> > > Subject: Re: [gmx-users] trjconv index file > > To: "Discussion list for GROMACS users" <[email protected]> > > Date: Tuesday, June 15, 2010, 6:10 PM > > > > > > > > ----- Original Message ----- > > From: Rabab Toubar <[email protected]> > > Date: Wednesday, June 16, 2010 1:44 > > Subject: [gmx-users] trjconv index file > > To: Discussion list for GROMACS users <[email protected]> > > > >> 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 > > ======================================== > -- gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use > the www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
