[gmx-users] can gromacs read amber trajectory

[Lydia]

   Amber mdcrd trajectory has the same format of .g87 (title, x(i) and box).

   I tried g_hbond -e 750 but it gave me the same. I notice that in the
manual, you have .g96 instead .g87 mostly. Is it because .g87 can not be
read and analyzed any more?  Thank you for your help and information.

sincerely
Lydia
On 2/18/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> 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
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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