----- Original Message ----- From: Rabab Toubar <rtou...@yahoo.com> Date: Wednesday, June 16, 2010 21:10 Subject: Re: [gmx-users] trjconv index file To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Mark Abraham <mark.abra...@anu.edu.au>
> 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 > > Am I missing something? Yes. Your email is missing copied and pasted input and output :-) Your spelling mistake in "trjconv" is a giveaway. Mark > 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----- > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php