[gmx-users] Re: g_hbond

[David van der Spoel]

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* < feenstra at few.vu.nl 
> <mailto: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) *
>       _____________ _______________________________________________________
>     |             |                                                       |
>     |  _   _  ___,| K. Anton Feenstra                                     |
>     | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
>     |(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands  |
>     | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
>     |             | Feenstra at few.vu.nl <mailto:Feenstra at few.vu.nl> -
>     www.few.vu.nl/~feenstra/ <http://www.few.vu.nl/~feenstra/>         |
>     |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
>     |_____________|_______________________________________________________|
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     <http://www.gromacs.org/mailman/listinfo/gmx-users>
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++