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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>The error tells you what the problem is:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='background:yellow'>Fatal error: reading tpx
file (em.tpr) version 40 with version 20 program</span><br>
<br>
<span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>You are trying to read an em.tpr file that was generated using
version 40 (as noted by the header it is GROMACS 3.3.1) using a version 20
program (as noted by the header it is GROMACS 3.0.5). You have to use a
program that is at least 3.3.1 for it to work. Would be better if you were
using the current 4.0.x version.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Department of Pharmaceutical Biology <br>
Pharmacy and Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>s lal badshah<br>
<b>Sent:</b> Wednesday, 8 July 2009 8:17 AM<br>
<b>To:</b> gromacs<br>
<b>Subject:</b> [gmx-users] Fatal error<o:p></o:p></span></p>
</div>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Hi gromacs users,<br>
<br>
the other fatal error which is produces from my last year data is:<br>
syed@linux-g1cj:~/Desktop/283> g_rms -s em.tpr -f md283.trr -o
md283-rmsd.xvg<br>
:-) G R O M A C S (-:<br>
<br>
GROningen MAchine for Chemical Simulation<br>
<br>
:-) VERSION 3.0.5 (-:<br>
<br>
Copyright (c) 1991-2001, University of
Groningen, The Netherlands<br>
This program is free
software; you can redistribute it and/or<br>
modify it under the
terms of the GNU General Public License<br>
as published by the Free
Software Foundation; either version 2<br>
of
the License, or (at your option) any later version.<br>
<br>
:-) g_rms (-:<br>
<br>
Option Filename
Type Description<br>
------------------------------------------------------------<br>
-s em.tpr
Input Structure+mass(db): tpr
tpb tpa gro g96 pdb<br>
-f md283.trr
Input Generic trajectory: xtc
trr trj gro g96 pdb<br>
-f2 traj.xtc Input,
Opt. Generic trajectory: xtc trr trj gro g96 pdb<br>
-n index.ndx Input,
Opt. Index file<br>
-o md283-rmsd.xvg
Output xvgr/xmgr file<br>
-mir rmsdmir.xvg Output, Opt. xvgr/xmgr file<br>
-a avgrp.xvg Output, Opt.
xvgr/xmgr file<br>
-dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file<br>
-m rmsd.xpm Output,
Opt. X PixMap compatible matrix file<br>
-bin rmsd.dat Output, Opt.
Generic data file<br>
-bm bond.xpm Output,
Opt. X PixMap compatible matrix file<br>
<br>
Option Type Value
Description<br>
------------------------------------------------------<br>
-[no]h
bool no Print help info and quit<br>
-[no]X
bool no Use dialog box GUI to edit command line
options<br>
-nice
int 19 Set the nicelevel<br>
-b
time -1 First frame (ps) to read from
trajectory<br>
-e
time -1 Last frame (ps) to read from trajectory<br>
-dt
time -1 Only use frame when t MOD dt = first
time (ps)<br>
-tu
enum ps Time unit: ps, fs, ns, us, ms, s, m or
h<br>
-[no]w
bool no View output xvg, xpm, eps and pdb files<br>
-what enum
rmsd Structural difference measure: rmsd, rho or rhosc<br>
-[no]pbc bool yes PBC
check<br>
-[no]fit bool yes Fit
to reference structure<br>
-prev
int 0 Compare with previous frame<br>
-[no]split bool no Split
graph where time is zero<br>
-skip
int 1 Only write every nr-th frame to
matrix<br>
-skip2
int 1 Only write every nr-th frame to
matrix<br>
-max
real -1 Maximum level in comparison matrix<br>
-min
real -1 Minimum level in comparison matrix<br>
-bmax
real -1 Maximum level in bond angle matrix<br>
-bmin
real -1 Minimum level in bond angle matrix<br>
-nlevels int
80 Number of levels in the matrices<br>
<br>
<span style='background:yellow'>Reading file em.tpr, VERSION 3.3.1 (single
precision)</span><br>
<span style='background:yellow'>Fatal error: reading tpx file (em.tpr)
version 40 with version 20 program</span><br>
<br>
So now whats the main problem with this data:<o:p></o:p></p>
<div>
<p class=MsoNormal><b><span style='color:#007F40'><br>
<strong>Regards,</strong></span></b><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><strong><span style='color:#007F40'>LAL BADSHAH </span></strong><o:p></o:p></p>
</div>
</td>
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</table>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
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