MGiò wrote:
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)
If this was 3.2.1 it's fixed in 3.3
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* < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
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