Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 31 12:35:52 CEST 2010
Nilesh Dhumal wrote:
> 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
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.
> On Mon, August 30, 2010 10:47 pm, Justin A. Lemkul wrote:
>> Nilesh Dhumal wrote:
>>> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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