VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 28 2011 - 10:01:43 CDT

please stop reposting the same question in close succession.
there is no reason for it and it is very annoying.

thanks,
    axel.

On Wed, Sep 28, 2011 at 10:05 AM, oguz gurbulak <gurbulakoguz_at_yahoo.com> wrote:
> 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.
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.