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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