Hey, In cases where you do end up with two index files, like resulting from a script or so, you can also simply combine them by concatenation:
cat A.ndx B.ndx > C.ndx Of course you'll have to make sure that the group names are unique ;) Cheers, Tsjerk 2012/1/10 ahmet yıldırım <ahmedo...@gmail.com>: > Thanks Mark and Marzinek, > > The Problem is solved: > > g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx > >> chain A > > Found 1234 atoms with chain identifier A > > 19 chA : 1234 atoms > >> name 19 chainA > > >> chain B > > Found 1234 atoms with chain identifier B > > 20 chB : 1234 atoms > >> name 20 chainB > > >> q > > > 2012/1/10 Marzinek, Jan <j.marzine...@imperial.ac.uk> >> >> So as you can see Gromacs does not support multi file input :) Create one >> index file and specify there your two groups. Then g_hbond will ask you to >> choose two groups from this file. >> >> >> >> Jan >> >> >> >> >> =========================================================== >> Jan Marzinek >> PhD Candidate >> Centre for Process Systems Engineering >> Department of Chemical Engineering >> Imperial College London >> South Kensington Campus >> London SW7 2AZ >> E: j.marzine...@imperial.ac.uk >> M: +44(0)7411 640 552 >> ________________________________ >> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on >> behalf of ahmet yıldırım [ahmedo...@gmail.com] >> Sent: Tuesday, January 10, 2012 8:13 AM >> To: Discussion list for GROMACS users >> Subject: [gmx-users] multi file input for index files >> >> Dear users, >> >> I created two different index files (A.ndx and B.ndx). I want to run the >> two files at the same time. >> e.g. >> g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx >> where, I want to calculate the hydrogen bonds between A and B. >> This command is giving the error as it expected. "Gromacs tools do not >> support multi file input for index files" from >> http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. >> Is this correct? If no, what should I do? >> >> Thanks in advance >> -- >> Ahmet Yıldırım >> >> >> -- >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > > -- > Ahmet Yıldırım > > > -- > 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/Support/Mailing_Lists/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/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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
