Hello gromacs users,
The default output file of gmx hbond is summary_HBmap.dat.
I do different types of gmx hbond analysis, for which I need output .dat files with different names.
I tried -o summary_HBmap04.dat in the gmx hbond command, but this did not work.
Is there a way for this?
Many thanks,
Neena
gmx hbond produces no such file; that looks more like the output of my post-processing script.
Please be more specific than “this did not work” as that’s not information we can use to troubleshoot. What happened? I suspect you got a fatal error because -o is not a valid option for gmx hbond. Consult the help information for appropriate command-line arguments.
Thanks for pointing that out, yes summary_HBmap.dat is an output file of the perl script you wrote for H-bond occupancy
My goal here was to do gmx hbond using 0.4 nm as the X-H…Acceptor distance as cut off (in addition to default 0.35 nm) and then I tried perl plot_hbmap_generic.pl -s em1.pdb -map hbmap_04.xpm -index hbond_04.ndx -o summary_HBmap_04.dat
Although the output file is still saved as summary_HBmap.dat, it does contain both old and new H-bond occupancy values listed in order.
So I think my problem is solved, thank you!
Just as an FYI on this, there is no -o option to my script; the output is always written to summary_HBmap.dat, though it is trivial to modify this on your own if greater flexibility is needed.