erikm at xray.bmc.uu.se
Tue Aug 31 14:44:20 CEST 2010
Justin A. Lemkul skrev 2010-08-31 12.35:
> 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
> 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.
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.
>> 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
>>>> 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
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at http://www.gromacs.org/search before
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org. Can't
>>> post? Read
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
More information about the gromacs.org_gmx-users