VMD-L Mailing List

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Thu Sep 29 2011 - 06:15:12 CDT

  Dear Axel, Thanks for your help. I solved the problem and composed tpr file successfully. And I tried to compose one more tpr file for my another system. I generated the tpr file but also I saw some notes on terminal. Do any of these notes will cause a problem when making analysis ? Should I consider them ? Thank you very much for your attention. Best regards ************* Generated 105 of the 105 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 105 of the 105 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'molecule0' Excluding 3 bonded neighbours molecule type 'molecule1' Excluding 3 bonded neighbours molecule type 'molecule2' NOTE 1 [file gromacs.top, line 292]: System has non-zero total charge: -4.000000e-03 NOTE 2 [file gromacs.top]: The largest charge group contains 14 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. NOTE 3 [file gromacs.top]: The largest charge group contains 14 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 1040 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 11277.00 Largest charge group radii for Coulomb: 0.535, 0.535 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 21x21x168, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.34 This run will generate roughly 89 Mb of data There were 3 notes Are these notes ********* ________________________________ From: oguz gurbulak <gurbulakoguz_at_yahoo.com> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu> Sent: Wednesday, September 28, 2011 5:05 PM Subject: vmd topotools 1.2 error Dear All, I'm trying to compose a tpr file in order to use some gmx 4.5 tools like g_rdf, g_order, g_msd, g_hbond. To do it I composed a top file using psf and dcd files with topotools1.2 in vmd . Then I used the command grompp_d -f min.mdp -c complex.pdb -p complex.top -o complex.tpr and saw this error:    :-) G R O M A C S (-:    GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 4.5.4 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. 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. :-) grompp_d (double precision) (-: Option Filename Type Description ------------------------------------------------------------ -f min.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c complex.pdb Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p complex.top Input Topology file -pp processed.top Output, Opt. Topology file -o complex.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 703 of the 703 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 703 of the 703 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'molecule0' Excluding 3 bonded neighbours molecule type 'molecule1' Excluding 3 bonded neighbours molecule type 'molecule2' Excluding 3 bonded neighbours molecule type 'molecule3' Excluding 3 bonded neighbours molecule type 'molecule4' ERROR 1 [file complex.top, line 18785]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. ------------------------------------------------------- Program grompp_d, VERSION 4.5.4 Source code file: grompp.c, line: 1370 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Can't You Make This Thing Go Faster ?" (Black Crowes) I also used any min.mdp file that is not important for analysis. But I couldn't solve the error in top to compose a tpr file. How can I reach this problem ? Could you please help me about this issue ? However, do I need to generate a .ndx file for each gmx analysis tools ? make_ndx -f complex.tpr -o complex.ndx ( for example ) All related files can be downloaded from the link http://www.speedyshare.com/files/30510532/files.tar.gz Thank you very much for your attention. Kind regards.