Re: [gmx-users] Error in Analysis Script RMSD

[Arneh Babakhani]

Ahh yes, you're right.  The script is in the right directory, but for 
some reason it keeps reverting back to my home directory.  I threw in a 
cd line to fix it.  Thanks for the help!

Arneh
Mark Abraham 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.

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
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