[gmx-users] Error in Analysis Script RMSD

[Mark Abraham]

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.

Ahh, but we trust the functionality of g_rms opening files (which is 
presumably common to all the gromacs tools) more than we trust you :-) 
Where is the script located, how are you running it and where are you 
running it from? Put a pwd command at the top to help diagnose what's 
happening.

The script itself looks fine at a casual glance.

Mark