[gmx-users] can gromacs read amber trajectory

Lydia aether2006 at gmail.com
Sat Feb 18 20:56:06 CET 2006 

    I'm checking.  For box, is it 3*10 or 3*8 per frame? I do see difference
in the defined format between .g87 and amber for the box as the following:
For .g87:

--------------------------------------------------------------------------
TITLE
x(i) (10f8.3)
box(m) (10f8.8)
----------------------------------------------------------------------------


For amber:
---------------------------------------------------------------------------------------
 AMBER trajectory (coordinate or velocity) file specification  This file is
optionally written during dynamics in SANDER or GIBBS.

FORMAT(20A4) ITITL
  ITITL  : the title of the current run, from the AMBER
           parameter/topology file

The following snapshot is written every NTWX steps in the trajectory
(specified in the control input file):

FORMAT(10F8.3)  (X(i), Y(i), Z(i), i=1,NATOM)
  X,Y,Z  : coordinates or velocities (velocity units: Angstroms per 1/20.455 ps)

IF constant pressure (in 4.1, also constant volume) For each snapshot:

FORMAT(10F8.3)  BOX(1), BOX(2), BOX(3)
---------------------------------------------------------------------------------------



sincerely
lydia

On 2/18/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Lydia wrote:
> >    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.
>
> Then you'll have to debug a bit further. I suspect the file and the
> software go out of sync somewhere. Does it work to read 100 frames? 10
> frames? 1 frame? (Use the -e option again).
>
> You should be able to read 1 frame and compute hbonds on it.
>
> Also you could try to check the file size. If you have Natom atoms then
> the file size should be Natom*3*8 bytes + 3*10 bytes (box) per frame,
> plus 80 bytes for  a title. Thus
> Filesize = 80 + Nframe * ( Natom*3*8 + 3*10 )
> It might be that an extra character is stored per line in the file
> (newline), this you could take into account by subtracting the number of
> lines in the file (wc file.g87)
>
> Good luck...
>
> > Lydia
> >
> > On 2/18/06, *Lydia* <aether2006 at gmail.com <mailto: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
> >     <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> >         spoel at gromacs.org <mailto:spoel at gromacs.org>
> >         http://xray.bmc.uu.se/~spoel <http://xray.bmc.uu.se/%7Espoel>
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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> >
> >
> > ------------------------------------------------------------------------
> >
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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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