Justin A. Lemkul skrev 2010-08-31 12.35:
Nilesh Dhumal wrote:
THanks.
I have one more system dioxin + water molecules. There is possiblity of
C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
I want to calculate the number of hydrogen bonds.
I used the following command
g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr -n dix-bdmp-no.ndx -num
I selected the hydrogen atom and oxygen atom of water
Igot this error
Checking for overlap in atoms between H96 and O21
Calculating hydrogen bonds between H96 (4 atoms) and O21 (256 atoms)
Found 0 donors and 256 acceptors
No Donors found
-------------------------------------------------------
Program g_hbond, VERSION 4.0.5
Source code file: gmx_hbond.c, line: 2235
Fatal error:
Nothing to be done
Two problems:
1. As g_hbond states, you don't have any donors. It is insufficient
to supply only H atoms in the "donor" group, since g_hbond needs to
calculate geometric parameters related to the D-H...A angle, so the
heavy atom to which the H is connected must be included in this group
as well.
2. I don't believe g_hbond will recognize any hydrogen bonds involving
CH species.
-Justin
It is true what Justin says. However, you can circumvent the first
problem partialy with the -contact option. Note however that the angular
component is lost with -contact.
Increased user control over donors and acceptors (solving problem number
two in Justin's post) is on the wishlist, but so are many other things.
Eventually it will be implemented, but I can't say when.
Nilesh
On Mon, August 30, 2010 10:47 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I have a system with a glucose molecule and 256 water molecules.
I want to find out the number of hydrogen bond between the hydrogen
atom
of OH group of glucose and the oxygen atom of water. How can I make
the index file.
Type "help" at the make_ndx prompt for examples. These groups are very
easy to create by specifying the desired atom names.
-Justin
Thanks
NIlesh
--
========================================
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
========================================
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