Hi All, I have MD simulation which crashed and I combine the frames with trjconv. Now the problem is that when I do analysis like that of Solvent accessible surface area, it showed that the incomplete frame . I use the gmxcheck with the following result d 1: 'Protein' 1695 out of 2854 atoms were classified as hydrophobic Reading frame 20 time 400.000 WARNING: Incomplete frame: nr 28 time 560
gcq#190: "That Was Cool" (Beavis and Butthead) [EMAIL PROTECTED]:~/323> gmxcheck -f md323.xtc -s1 md323.tpr -e md323.edr :-) G R O M A C S (-: Glycine aRginine prOline Methionine Alanine Cystine Serine :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) gmxcheck (-: Option Filename Type Description ------------------------------------------------------------ -f md323.xtc Input, Opt! Generic trajectory: xtc trr trj gro g96 pdb -f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -s1 md323.tpr Input, Opt! Generic run input: tpr tpb tpa xml -s2 top2.tpr Input, Opt. Generic run input: tpr tpb tpa xml -c topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb xml -e md323.edr Input, Opt! Generic energy: edr ene -e2 ener2.edr Input, Opt. Generic energy: edr ene -n index.ndx Input, Opt. Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -vdwfac real 0.8 Fraction of sum of VdW radii used as warning cutoff -bonlo real 0.4 Min. fract. of sum of VdW radii for bonded atoms -bonhi real 0.7 Max. fract. of sum of VdW radii for bonded atoms -tol real 0.001 Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) -[no]ab bool no Compare the A and B topology from one file -lastener string Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. Reading file md323.tpr, VERSION 3.3.1 (single precision) Checking file md323.xtc Reading frame 0 time 0.000 # Atoms 37959 Precision 0.001 (nm) Reading frame 20 time 400.000 WARNING: Incomplete frame: nr 28 time 560 Item #frames Timestep (ps) Step 28 20 Time 28 20 Lambda 0 Coords 28 20 Velocities 0 Forces 0 Box 28 20 Checking energy file md323.edr Opened md323.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last frame read 500 time 1000.000 Found 501 frames with a timestep of 2 ps. gcq#58: "You Look Better Upside Down" (Throwing Muses) Now what should I do? Please guide me. SYED LAL BADSHAH Send instant messages to your online friends http://uk.messenger.yahoo.com
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