[gmx-users] Error in Analysis Script RMSD

[Marco Pasi]

On 5/23/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Arneh Babakhani wrote:
> > Hi,
> >
> > I'm experiencing an awkward error.  I created an analysis script to
> > calculate some RMSDs (I've pasted the script below).
> > When I try to run the script, I get an error.  The following is the output.
> > Option     Filename  Type         Description
> > ------------------------------------------------------------
> >  -s ../../FullMD/FullMD1.tpr  Input        Structure+mass(db): tpr tpb tpa
> >                                   gro g96 pdb xml
> >  -f ../../FullMD/FullMD1.trr  Input        Generic trajectory: xtc trr trj
> >                                   gro g96 pdb
> > -f2       traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro g96
> > pdb
> >  -n ActiveSites.ndx  Input, Opt!  Index file
> >  -o  ChainAB-1.xvg  Output       xvgr/xmgr file
> > -mir    rmsdmir.xvg  Output, Opt. xvgr/xmgr file
> >  -a      avgrp.xvg  Output, Opt. xvgr/xmgr file
> > -dist rmsd-dist.xvg  Output, Opt. xvgr/xmgr file
> >  -m       rmsd.xpm  Output, Opt. X PixMap compatible matrix file
> > -bin       rmsd.dat  Output, Opt. Generic data file
> > -bm       bond.xpm  Output, Opt. X PixMap compatible matrix 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)
> >         -tu   enum     ps  Time unit: ps, fs, ns, us, ms or s
> >      -[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
> >       -what   enum   rmsd  Structural difference measure: rmsd, rho or
> > rhosc
> >    -[no]pbc   bool    yes  PBC check
> >        -fit   enum rot+trans  Fit to reference structure: rot+trans,
> >                            translation or none
> >       -prev    int      0  Compare with previous frame
> >  -[no]split   bool     no  Split graph where time is zero
> >       -skip    int      1  Only write every nr-th frame to matrix
> >      -skip2    int      1  Only write every nr-th frame to matrix
> >        -max   real     -1  Maximum level in comparison matrix
> >        -min   real     -1  Minimum level in comparison matrix
> >       -bmax   real     -1  Maximum level in bond angle matrix
> >       -bmin   real     -1  Minimum level in bond angle matrix
> >     -[no]mw   bool    yes  Use mass weighting for superposition
> >    -nlevels    int     80  Number of levels in the matrices
> >         -ng    int      1  Number of groups to compute RMS between
> >
> > -------------------------------------------------------
> > Program g_rms, VERSION 3.3.1
> > Source code file: gmxfio.c, line: 706
> >
> > Can not open file:
> > ../../FullMD/FullMD1.tpr
> > -------------------------------------------------------
> >
> >
> > I'm not sure why the script cannot open this tpr file.  It is there,
> > trust me.
>
> I don't trust you :). The script may be in another directory than you
> think it is, e.g. because you cd into a non-existant directory.
>
> > When I run the g_rms tool from the command line (as it appears in the
> > script), everything works fine.  It just can't open the tpr file, /when
> > run from the script/.   Any ideas what's going on here????  Thanks,
> >
> >
>
> --
> 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://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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Hi,

you might find it useful to try running 'ls ../../' in your script to
check the contents of the directory from inside the script;
furthermore if you run 'whoami' in the script you'll make sure what
user is trying to access the file, and check the tpr permissions
accordingly.  No more ideas come to mind on what could be happening.

Marco