[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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