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? 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----- -- 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
