Steven Neumann wrote:
One question.... for Glycine it is easy to assess 3 possible hbonds
which can create as hydrogen is only one atom as a side chain.
How about other amino acids and their maximum hbonds they can create?
Any OH or NH group is a donor, any lone pair is an acceptor (though obviously
not modeled explicitly in MD). The ability of MD force fields to agree with
reality in this respect is debatable, but should come close.
-Justin
Steven
On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann <s.neuman...@gmail.com
<mailto:s.neuman...@gmail.com>> wrote:
Thank you for clarification Justin!!! The Manual is not as clear as
you :P
Steven
On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
-- ==============================______==========
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/>
<http://vt.edu/> <http://vt.edu/> | (540)
231-9080 <tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem
<http://www.bevanlab.biochem/>.
<http://www.bevanlab.biochem./__>____vt.edu/Pages/Personal/__justin
<http://vt.edu/Pages/Personal/justin>
<http://vt.edu/Pages/Personal/__justin
<http://vt.edu/Pages/Personal/justin>>
<http://www.bevanlab.biochem.
<http://www.bevanlab.biochem./>____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<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 <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>__>
http://lists.gromacs.org/______mailman/listinfo/gmx-users
<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<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>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<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
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-request@
<mailto:gmx-users-request@>__gr__omacs.org <http://gromacs.org/>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
Can't post? Read
http://www.gromacs.org/______Support/Mailing_Lists
<http://www.gromacs.org/____Support/Mailing_Lists>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/__Support/Mailing_Lists
<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.
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?
No. The second column is not inclusive of the first. It
counts the
number of atoms that are within hydrogen bonding
distance, but do
not meet the criteria because of the angle between D-H-A.
-Justin
In this case number of collisions has to include number
of hbonds.
If collision is counted as a distance <3.5 and hbond
distance <3.5
plus angle D-H-A means that collisions covers hbonds...
Explain
please whether I am wrong.
The second column lists the number of atom pairs that satisfy
the distance requirement but do not satisfy the angle
requirement and therefore are not hydrogen bonds. The two
columns are mutually exclusive. The sum of these two columns
would be the total number of pairs that are within
hydrogen-bonding distance, but the first column indicates those
that are actually involved in hydrogen bonds (because of the
angle), and the second column indicates those that are not
involved in 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 <http://vt.edu/> | (540) 231-9080
<tel:%28540%29%20231-9080>
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
<mailto: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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
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
