[gmx-users] can gromacs read amber trajectory

[Lydia]

   I don't want to rerun because there are too many to rerun.  But I still
want to use gromacs analysis tool  which is very powerful.
Lydia

On 2/18/06, Lydia <aether2006 at gmail.com> wrote:
>
>    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
> > >
> > >
> > >
> > ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > 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<http://xray.bmc.uu.se/%7Espoel>
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > 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
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060218/e299dc35/attachment.html>