Hi Albert, pdb is mentioned valid input for both -f (trajectory) and -s (reference). So you can use the file you have for both:
g_cluster -s disco.pdb -f disco.pdb [...] Cheers, Tsjerk On Tue, Apr 3, 2012 at 8:23 AM, Albert <[email protected]> wrote: > Dear: > > I've generated a disoc.pdb file by concoord and does any one have any > idea how to analyze it by Gromacs g_cluster? when I read the manual of > g_cluter, it will require > > -f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt > -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb > -n index.ndx Input, Opt. Index file > -dm rmsd.xpm Input, Opt. X PixMap compatible matrix file > > > but the concoord output is a single pdb file..... > > thank you very much > > best wishes > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
