ndhumal at andrew.cmu.edu
Tue Aug 31 05:18:12 CEST 2010
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
Nothing to be done
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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