[gmx-users] Error in Analysis Script RMSD

[Arneh Babakhani]

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. 

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,



Here's the script (it's a single file that I'm trying to execute):

#!/bin/csh
set begtraj = 1
set entraj = 21
set NMBR = $begtraj

while ($NMBR < $entraj)
g_rms -f ../../FullMD/FullMD$NMBR.trr -s ../../FullMD/FullMD1.tpr -n 
ActiveSites.ndx -o ChainAB-$NMBR <<+
0
0
+
g_rms -f ../../FullMD/FullMD$NMBR.trr -s ../../FullMD/FullMD1.tpr -n 
ActiveSites.ndx -o ChainBC-$NMBR <<+
1
1
+
g_rms -f ../../FullMD/FullMD$NMBR.trr -s ../../FullMD/FullMD1.tpr -n 
ActiveSites.ndx -o ChainCD-$NMBR <<+
2
2
+
g_rms -f ../../FullMD/FullMD$NMBR.trr -s ../../FullMD/FullMD1.tpr -n 
ActiveSites.ndx -o ChainDE-$NMBR <<+
3
3
+
g_rms -f ../../FullMD/FullMD$NMBR.trr -s ../../FullMD/FullMD1.tpr -n 
ActiveSites.ndx -o ChainEA-$NMBR <<+
4
4
+
  set NMBR = `expr $NMBR + 1`
end