[gmx-users] Re: g_hbond

[MGiò]

Well,
this was my command line:

g_hbond -f ../../traj_c.trr -s ../../topol.tpr -g -num -dist -ang -hbn

and this was my screen output

No option -da
Reading file ../../topol.tpr, VERSION 3.2.1 (single precision)
Specify 2 groups to analyze:
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 25707 elements
Group     1 (     Protein) has  2462 elements
Group     2 (   Protein-H) has  1975 elements
Group     3 (     C-alpha) has   247 elements
Group     4 (    Backbone) has   741 elements
Group     5 (   MainChain) has   989 elements
Group     6 (MainChain+Cb) has  1226 elements
Group     7 ( MainChain+H) has  1230 elements
Group     8 (   SideChain) has  1232 elements
Group     9 ( SideChain-H) has   986 elements
Group    10 ( Prot-Masses) has  2462 elements
Group    11 ( Non-Protein) has 23245 elements
Group    12 (         EST) has    25 elements
Group    13 (         SOL) has 23220 elements
Group    14 (       Other) has 23245 elements
Select a group: 1
Selected 1: 'Protein'
Select a group: 12
Selected 12: 'EST'
Checking for overlap...
Calculating hydrogen bonds between two groups of 2462 and 25 atoms
Found 349 donors and 692 acceptors in group 'Protein'
Found 2 donors and 2 acceptors in group 'EST'
Going to allocate 5709 kb of memory,  and that's only the beginning
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Will do grid-seach on 16x15x14 grid, rcut=0.35
Last frame        100 time 3000.000
Found 5 different hydrogen bonds in trajectory
Merging hbonds with Acceptor and Donor swapped
Reduced number of hbonds from 5 to 5
tested 1394 pairs
Average number of hbonds per timeframe 1.218 out of 1041 possible

Any idea? The screen output seems correct to me, but for the fact that it
always says "no -da option" whether I use this option or not, why this?.
Thanks for any help.

MGiò





On 2/28/06, Anton Feenstra <feenstra at few.vu.nl> wrote:
>
> MGiò wrote:
>
> > Thanks, Kia,
> > actually I have used an index.ndx file, but the output is the same. I'll
> try
> > anyway with the automated procedure by the shell script. Thank you
> anyway
>
> The script does exactly the same as what you do manually. SO that won't
> help...
>
> Can you send the screen output of g_hbond?
>
>
> --
> Groetjes,
>
> Anton
>
> * NOTE: New Affiliation, Phone & Fax numbers (below) *
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> |  _   _  ___,| K. Anton Feenstra                                     |
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