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

[David van der Spoel]

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