Hi Justin, Thank you for the perl script. But I wonder now why there is a difference between what shows in the hbmap.xpm file and the summary_HBmap.dat generated.
For example, I found many occurrences of the second to last H-bond in the 20hbmap.xpm file attached (visualized by GIMP), but in the summary_HBmap.dat file there showed only 0.1 % Exist. of this specific H-bond. Anything wrong with my interpretation? Please see attached the files I used/ generated. Thanks, Yun On Sat, May 5, 2012 at 10:43 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 5/5/12 1:22 PM, Yun Shi wrote: > >> Hello all, >> >> I have used g_hbond with -hbn option to generate a .ndx file that has >> Acceptor - >> Donor - Hydrogen in each line of the last index group. >> >> But I wonder I could I use this index file to monitor each hydrogen bond >> specified by these triplets along the trajectory? >> >> > Depending on what you're trying to do, you can map the triplets in > hbond.ndx with the hbmap.xpm file to obtain, for instance, the % of total > frames that a particular hydrogen bond exists. I've done something along > those lines with a script I call plot_hbmap.pl, available from: > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**scripts.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html> > > Please note the usage information in the header of the file. > > > Also, I understand that the -ins in no longer available. But how can we >> analyze >> those water-mediated hydrogen bonds? >> >> > Doing something like this will require careful use of index groups and > external scripting. Presumably, if you have two groups (let's call them A > and B), if group A forms hydrogen bonds to a certain group of SOL residues, > and if group B does the same, with some of those SOL molecules overlapping > in some given frames, you can make an argument for a water-mediated > hydrogen bond. Determining the existence of the hydrogen bonds is easy with > g_hbond and index groups. Determining simultaneous occurrence requires an > external script, and can make use of hbmap.xpm (to determine which frames > contain the hydrogen bonds) and hbond.ndx (to determine which groups are > participating in those hydrogen bonds). > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > 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> >
<<attachment: 20hbmap.xpm>>
summary_HBmap.dat
Description: Binary data
mod_hb.ndx
Description: Binary data
-- 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