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<mailto: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
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