<span style="font-style: italic;">Well,</span><br style="font-style: italic;"><span style="font-style: italic;">this was my command line:</span><br style="font-style: italic;"><br>g_hbond -f ../../traj_c.trr -s ../../topol.tpr -g -num -dist -ang -hbn
<br><br><span style="font-style: italic;">and this was my screen output </span><br><br>No option -da<br>Reading file ../../topol.tpr, VERSION 3.2.1 (single precision)<br>Specify 2 groups to analyze:<br>Opening library file /usr/local/share/gromacs/top/aminoacids.dat
<br>Group 0 ( System) has 25707 elements<br>Group 1 ( Protein) has 2462 elements<br>Group 2 ( Protein-H) has 1975 elements<br>Group 3 ( C-alpha) has 247 elements<br>Group 4 ( Backbone) has 741 elements
<br>Group 5 ( MainChain) has 989 elements<br>Group 6 (MainChain+Cb) has 1226 elements<br>Group 7 ( MainChain+H) has 1230 elements<br>Group 8 ( SideChain) has 1232 elements<br>Group 9 ( SideChain-H) has 986 elements
<br>Group 10 ( Prot-Masses) has 2462 elements<br>Group 11 ( Non-Protein) has 23245 elements<br>Group 12 ( EST) has 25 elements<br>Group 13 ( SOL) has 23220 elements<br>Group 14 ( Other) has 23245 elements
<br>Select a group: 1<br>Selected 1: 'Protein'<br>Select a group: 12<br>Selected 12: 'EST'<br>Checking for overlap...<br>Calculating hydrogen bonds between two groups of 2462 and 25 atoms<br>Found 349 donors and 692 acceptors in group 'Protein'
<br>Found 2 donors and 2 acceptors in group 'EST'<br>Going to allocate 5709 kb of memory, and that's only the beginning<br>trn version: GMX_trn_file (single precision)<br>Reading frame 0 time 0.000<br>Will do grid-seach on 16x15x14 grid, rcut=
0.35<br>Last frame 100 time 3000.000<br>Found 5 different hydrogen bonds in trajectory<br>Merging hbonds with Acceptor and Donor swapped<br>Reduced number of hbonds from 5 to 5<br>tested 1394 pairs<br>Average number of hbonds per timeframe
1.218 out of 1041 possible<br><br><span style="font-style: italic;">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.
</span><br style="font-style: italic;"><br><span style="font-style: italic;">MGiò</span><br><br><br><br><br><br><div><span class="gmail_quote">On 2/28/06, <b class="gmail_sendername">Anton Feenstra</b> <<a href="mailto:feenstra@few.vu.nl">
feenstra@few.vu.nl</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">MGiò wrote:<br><br>> Thanks, Kia,<br>> actually I have used an
index.ndx file, but the output is the same. I'll try<br>> anyway with the automated procedure by the shell script. Thank you anyway<br><br>The script does exactly the same as what you do manually. SO that won't<br>help...
<br><br>Can you send the screen output of g_hbond?<br><br><br>--<br>Groetjes,<br><br>Anton<br><br>* NOTE: New Affiliation, Phone & Fax numbers (below) *<br> _____________ _______________________________________________________
<br>| | |<br>| _ _ ___,| K. Anton Feenstra |<br>| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
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