[gmx-users] pdb files from trajectory

2013-07-07 Thread Shima Arasteh
Dear gmx users, I' d like to get pdb files from trajectory, then used the trjconv, # trjconv -f trajout.xtc -o out.pdb -sep It gives fatal error as this: Can not open file: topol.tpr Sincerely, Shima  -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] pdb files from trajectory

2013-07-07 Thread Tsjerk Wassenaar
Hi Shima, You need to give a reference structure with the -s option. Otherwise the program assumes you mean to use topol.tpr, which isn't present. Cheers, Tsjerk On Sun, Jul 7, 2013 at 11:51 AM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Dear gmx users, I' d like to get pdb files

Re: [gmx-users] pdb files from trajectory

2013-07-07 Thread Mohsen Ramezanpour
Dear Shima What is the name of your .tpr file? If you had not chosen any name for it, Gromacs will generate a topol.tpr for you and in my idea this error will not occur, if not, you have to mention your file (e.g. Filename.tpr) explicitely in your command line! I hope this help you Best On Sun,