Steven Neumann wrote:
Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my ligands and
every single residue using g_hbond. Looking at the criteria adpoted by
Gromacs I found impossible that number of hydrogen bonds were higher
than number of collisions... And what is interesting in one of my
residue I obtained result like this... All Hbonds with Glycine - 1872,
All Collisions 704.
Does anyone know how is it possible?
I don't know how any of your numbers are possible (1872 H-bonds forming with a
glycine?), or what you are defining as a collision and how you calculated it.
Please provide the exact commands that you're using. If you're equating a
contact (e.g. from g_mindist) with a collision, then realize that the default
criteria for a contact are very different than the geometric criteria for a
hydrogen bond.
-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
========================================
--
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
