[gmx-users] Angle definition in g_hbond ...

[Anil Kumar]

Hi,

Just calculate the no. of atoms according to the choice of options and
manually. you will understand why is it giving the error.  Secondly check
how gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm
and 30 in version 3.3.1, but in earlier version the angle cut-off was 60 in
version 3.2 and 120 in version 3.1.

regards
anil
IITB, India

On Mon, May 5, 2008 at 7:20 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Mark Abraham wrote:
>
>> sharada wrote:
>>
>>> dear gmx-users,
>>>
>>> I have a very fundamental query. I am trying to obtain the backbone
>>> hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I
>>> do this by using g_hbond and selecting the Backbone groups, I am getting no
>>> hydrogen bonds at all . However, when I plot the hydrogen bonds for some of
>>> the structures picked up through the dynamics  using InsightII  I am able to
>>> see the backbone  HBs in almost all of them.
>>>
>>> This is the command I am using:
>>>
>>>  g_hbond -f  HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num
>>> hnum.xvg -g hb.log
>>>
>>> this is the output I obtain and the hb.log file is not created :
>>>
>>> Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision)
>>> Specify 2 groups to analyze:
>>> Group     0 (     Protein) has   358 elements
>>> Group     1 (   Protein-H) has   271 elements
>>> Group     2 (     C-alpha) has    36 elements
>>> Group     3 (    Backbone) has   108 elements
>>> Group     4 (   MainChain) has   144 elements
>>> Group     5 (MainChain+Cb) has   177 elements
>>> Group     6 ( MainChain+H) has   181 elements
>>> Group     7 (   SideChain) has   177 elements
>>> Group     8 ( SideChain-H) has   126 elements
>>> Group     9 ( Prot-Masses) has   358 elements
>>> Select a group: 3
>>> Selected 4: 'Backbone'
>>> Select a group: 3
>>> Selected 4: 'Backbone'
>>> Calculating hydrogen bonds in Backbone (108 atoms)
>>> Found 0 donors and 72 acceptors
>>> No Donors found
>>>
>>
>> I haven't used this tool, but the problem looks like it is here. Are there
>> any hydrogens in this group?
>>
>
> use 6
>
>
>> Mark
>> _______________________________________________
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>
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>
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ANIL KUMAR(Research Scholar),
Bio-Organic Lab No-336(2nd Floor),
Dept. of Chemistry,I.I.T.Bombay,Powai,
Mumbai-400076,
Ph. No.-022-25764780(Lab)
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