[gmx-users] can gromacs read amber trajectory

Lydia aether2006 at gmail.com
Sat Feb 18 16:43:33 CET 2006

   Thank you for your reply. I see box in the .g87 file. And if I try choice
3, I get the following and end up segementation fault again.

   g_gyrate -f nmwt.g87 -s nmwt.tpr -n index.ndx

                         :-)  G  R  O  M  A  C  S  (-:

              GROningen Mixture of Alchemy and Childrens' Stories

                             :-)  VERSION 3.3  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                               :-)  g_gyrate  (-:

Option     Filename  Type         Description
  -f       nmwt.g87  Input        Generic trajectory: xtc trr trj gro g96
  -s       nmwt.tpr  Input        Structure+mass(db): tpr tpb tpa gro g96
  -n      index.ndx  Input, Opt!  Index file
  -o     gyrate.xvg  Output       xvgr/xmgr file
-acf    moi-acf.xvg  Output, Opt. xvgr/xmgr file

      Option   Type  Value  Description
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int     19  Set the nicelevel
          -b   time      0  First frame (ps) to read from trajectory
          -e   time      0  Last frame (ps) to read from trajectory
         -dt   time      0  Only use frame when t MOD dt = first time (ps)
      -[no]w   bool     no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   bool    yes  Add specific codes (legends etc.) in the output
                            xvg files for the xmgrace program
       -nmol    int      1  The number of molecules to analyze
      -[no]q   bool     no  Use absolute value of the charge of an atom as
                            weighting factor instead of mass
      -[no]p   bool     no  Calculate the radii of gyration about the
                            principal axes.
    -[no]moi   bool     no  Calculate the moments of inertia (defined by
                            principal axes).
     -acflen    int     -1  Length of the ACF, default is half the number of
-[no]normalize bool    yes  Normalize ACF
          -P   enum      0  Order of Legendre polynomial for ACF (0
                            none): 0, 1, 2 or 3
      -fitfn   enum   none  Fit function: none, exp, aexp, exp_exp, vac,
                            exp5, exp7 or exp9
     -ncskip    int      0  Skip N points in the output file of correlation
   -beginfit   real      0  Time where to begin the exponential fit of the
                            correlation function
     -endfit   real     -1  Time where to end the exponential fit of the
                            correlation function, -1 is till the end

Reading file nmwt.tpr, VERSION 3.3 (single precision)
Reading file nmwt.tpr, VERSION 3.3 (single precision)
Group     0 (      System) has 17351 elements
Group     1 (     Protein) has   732 elements
Group     2 (   Protein-H) has   366 elements
Group     3 (     C-alpha) has    52 elements
Group     4 (    Backbone) has   156 elements
Group     5 (   MainChain) has   209 elements
Group     6 (MainChain+Cb) has   250 elements
Group     7 ( MainChain+H) has   260 elements
Group     8 (   SideChain) has   472 elements
Group     9 ( SideChain-H) has   157 elements
Group    10 ( Prot-Masses) has   732 elements
Group    11 ( Non-Protein) has 16619 elements
Group    12 (         Cl-) has     5 elements
Group    13 (         WAT) has 16614 elements
Group    14 (       Other) has 16619 elements
Select a group: 1
Selected 1: 'Protein'

   Select File Format
1. XYZ File
2. XYZ File with Box
3. Gromos-87 Ascii Trajectory
4. Gromos-87 Ascii Trajectory with Box

Choice: 3


Number of atoms ? 17351
Time between timeframes ? 1
Box X Y Z ?  6.40310    5.96850    4.57077

Reading frame     790 time  791.000   error reading statusfile: x[800][0]

Back Off! I just backed up gyrate.xvg to ./#gyrate.xvg.6#
Segmentation fault

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