[gmx-users] Can not open file:md323.xtc

[s lal badshah]

Hi All,
During analysis the following error also came;

mad at uop:~/project> g_rmsf -s md323.tpr -f md323.xtc -o rmsf.xvg -oq bfac.pdb
                         :-)  G  R  O  M  A  C  S  (-:

               Giant Rising Ordinary Mutants for A Clerical Setup

                            :-)  VERSION 3.3.1  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, 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_rmsf  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f      md323.xtc  Input        Generic trajectory: xtc trr trj gro g96 pdb
  -s      md323.tpr  Input        Structure+mass(db): tpr tpb tpa gro g96 pdb
                                   xml
  -n      index.ndx  Input, Opt.  Index file
  -q      eiwit.pdb  Input, Opt.  Protein data bank file
 -oq       bfac.pdb  Output, Opt! Protein data bank file
 -ox      xaver.pdb  Output, Opt. Protein data bank file
  -o       rmsf.xvg  Output       xvgr/xmgr file
 -od     rmsdev.xvg  Output, Opt. xvgr/xmgr file
 -oc     correl.xvg  Output, Opt. xvgr/xmgr file
-dir       rmsf.log  Output, Opt. Log file

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
       -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
    -[no]res   bool     no  Calculate averages for each residue
  -[no]aniso   bool     no  Compute anisotropic termperature factors
    -[no]fit   bool    yes  Do a least squares superposition before computing
                            RMSF. Without this you must make sure that the
                            reference structure and the trajectory match.

Reading file md323.tpr, VERSION 3.3.1 (single precision)
Reading file md323.tpr, VERSION 3.3.1 (single precision)
Select group(s) for root mean square calculation
Opening library file /usr/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 65725 elements
Group     1 (     Protein) has  5493 elements
Group     2 (   Protein-H) has  2796 elements
Group     3 (     C-alpha) has   347 elements
Group     4 (    Backbone) has  1041 elements
Group     5 (   MainChain) has  1390 elements
Group     6 (MainChain+Cb) has  1706 elements
Group     7 ( MainChain+H) has  1723 elements
Group     8 (   SideChain) has  3770 elements
Group     9 ( SideChain-H) has  1406 elements
Group    10 ( Prot-Masses) has  5493 elements
Group    11 ( Non-Protein) has 60232 elements
Group    12 (         SOL) has 60228 elements
Group    13 (         NA+) has     4 elements
Group    14 (       Other) has 60232 elements
Select a group: 3
Selected 3: 'C-alpha'
-------------------------------------------------------
Program g_rmsf, VERSION 3.3.1
Source code file: gmxfio.c, line: 706

Can not open file:
md323.xtc
-------------------------------------------------------
Whats the reason ?
Regards,
Lal badshah

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