Hi, But I want to calculate the hydrogen bonds between A and B groups. If I do as you said, I will have calculated intra hydrogen bonds of a group AB (merged A and B).
2012/1/10 Mark Abraham <mark.abra...@anu.edu.au> > On 10/01/2012 7:13 PM, ahmet yıldırım wrote: > >> 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<http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html>. >> Is this correct? If no, what should I do? >> > > You can put your two groups in the same index file. > > Run make_ndx and quit to see the format for index.ndx that it generates by > default. You can do that too. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım
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