Hi All,<br>During analysis the following error also came;<br><br>mad@uop:~/project> g_rmsf -s md323.tpr -f md323.xtc -o rmsf.xvg -oq bfac.pdb<br> :-) G R O M A C S (-:<br><br> Giant Rising Ordinary Mutants for A Clerical Setup<br><br> :-) VERSION 3.3.1 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The
Netherlands.<br> Copyright (c) 2001-2006, The GROMACS development team,<br> check out http://www.gromacs.org for more information.<br><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_rmsf
(-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f md323.xtc Input Generic trajectory: xtc trr trj gro g96 pdb<br> -s md323.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb<br> xml<br> -n index.ndx Input, Opt. Index file<br> -q eiwit.pdb Input, Opt. Protein data bank file<br> -oq bfac.pdb Output, Opt! Protein data bank
file<br> -ox xaver.pdb Output, Opt. Protein data bank file<br> -o rmsf.xvg Output xvgr/xmgr file<br> -od rmsdev.xvg Output, Opt. xvgr/xmgr file<br> -oc correl.xvg Output, Opt. xvgr/xmgr file<br>-dir rmsf.log Output, Opt. Log file<br><br> Option Type Value Description<br>------------------------------------------------------<br> -[no]h bool no Print help info and quit<br> -nice int 19 Set the nicelevel<br> -b time 0 First frame (ps) to
read from trajectory<br> -e time 0 Last frame (ps) to read from trajectory<br> -dt time 0 Only use frame when t MOD dt = first time (ps)<br> -[no]w bool no View output xvg, xpm, eps and pdb files<br> -[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace program<br> -[no]res bool no Calculate averages for each residue<br> -[no]aniso bool no Compute
anisotropic termperature factors<br> -[no]fit bool yes Do a least squares superposition before computing<br> RMSF. Without this you must make sure that the<br> reference structure and the trajectory match.<br><br>Reading file md323.tpr, VERSION 3.3.1 (single precision)<br>Reading file md323.tpr, VERSION 3.3.1 (single precision)<br>Select group(s) for root mean square calculation<br>Opening library file /usr/share/gromacs/top/aminoacids.dat<br>Group 0 ( System) has 65725 elements<br>Group 1 ( Protein)
has 5493 elements<br>Group 2 ( Protein-H) has 2796 elements<br>Group 3 ( C-alpha) has 347 elements<br>Group 4 ( Backbone) has 1041 elements<br>Group 5 ( MainChain) has 1390 elements<br>Group 6 (MainChain+Cb) has 1706 elements<br>Group 7 ( MainChain+H) has 1723 elements<br>Group 8 ( SideChain) has 3770 elements<br>Group 9 ( SideChain-H) has 1406 elements<br>Group 10 ( Prot-Masses) has 5493 elements<br>Group 11 ( Non-Protein) has 60232 elements<br>Group 12 ( SOL) has 60228 elements<br>Group 13
( NA+) has 4 elements<br>Group 14 ( Other) has 60232 elements<br>Select a group: 3<br>Selected 3: 'C-alpha'<br>-------------------------------------------------------<br>Program g_rmsf, VERSION 3.3.1<br>Source code file: gmxfio.c, line: 706<br><br>Can not open file:<br>md323.xtc<br>-------------------------------------------------------<br>Whats the reason ?<br>Regards,<br>Lal badshah<br><p> Send instant messages to your online friends http://uk.messenger.yahoo.com