Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 31 16:44:00 CEST 2011
Steven Neumann wrote:
> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> 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 A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
> My system is made of 10 ligands and one protein. I used command:
> g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
> Where I specified in the index file two groups: 10 ligands and Glycine
> residue. So I have calculated hbonds (second column) and collisions
> (third column) and then I made a sum of all frames during 100 ns
> simualtion time (one frame every 50 ps) obtaining 1872 hbonds and 703
> collisions between Glycine and 10 ligands. I did it with every residue
> to assess binding affinity of different amino acids.
I forgot to mention in the previous message that there is no value in summing
the hydrogen bonds over time. Some of those H-bonds may be distinct, and others
may be the same H-bond that has broken and subsequently re-formed. I doubt
anyone would find real value in saying that 10 ligands formed 1872 H-bonds with
glycine over a trajectory.
> Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A
> and angle. So when calcualting hbond and collisions the number of hbonds
> has has to be smaller while collision takes into account hbonds as
> welll. I obtained results like this for all other residues which seems
> to be correct. Am I right?
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users