[gmx-users] can gromacs read amber trajectory

[David van der Spoel]

Lydia wrote:
>     If I calculate hbond it won't  give error information but  the 

try g_hbond -e 750
to see whether the beginning of the traj is OK.

If the format is not as expected I don't know how to fix it. Maybe you 
can mould our trajecotry into another format using some kind of script. 
Otherwise just try and rerun the simulation...

> hbnum.xvg will be
> -----------------------------------------------------------------------------------------------------------------
> cat hbnum.xvg
> 
> # This file was created Sat Feb 18 08:44:34 2006
> # by the following command:
> # g_hbond -f nmwt.g87 -s nmwt.tpr -n index.ndx -num -hbm -a 120
> #
> # g_hbond is part of G R O M A C S:
> #
> # GRowing Old MAkes el Chrono Sweat
> #
> @    title "Hydrogen Bonds"
> @    xaxis  label "Time"
> @    yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>        801          11           4
> ----------------------------------------------------------------------------------------------------------------
>      I'm expecting 800 rows of numbers which are the number of hbonds 
> as  a function of time (800ps).  But it  has only one row to give out 
> the average number of hbonds per timeframe 11.000 out of 330 possible. 
> 
> Best wishes
> Lydia
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> 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://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++