[gmx-users] it may b a bug.....i dont know

uma reddy umamaheswar_kgp at yahoo.com
Mon Apr 16 22:49:50 CEST 2007

i am beginer to GROMACS. i am using the examples provided in the gromacs site. when i try to generate solvent model for speptide of ribonuclese s peptide then i encounter a problem stating 

yahoo at debian:~/gromacs/gromacs/tutor/speptide$ genbox -cp out -cs -p speptide -0 b4em
                         :-)  G  R  O  M  A  C  S  (-:

                              S  C  A  M  O  R  G

                            :-)  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.

                                :-)  genbox  (-:

Option     Filename  Type         Description
 -cp        out.gro  Input, Opt!  Generic structure: gro g96 pdb tpr tpb tpa
 -cs     spc216.gro  Input, Opt!, Lib. Generic structure: gro g96 pdb tpr tpb
                                   tpa xml
 -ci     insert.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
  -o        out.gro  Output       Generic structure: gro g96 pdb xml
  -p   speptide.top  In/Out, Opt! Topology file

      Option   Type  Value  Description
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int     19  Set the nicelevel
        -box vector  0 0 0  box size
       -nmol    int      0  no of extra molecules to insert
        -try    int     10  try inserting -nmol*-try times
       -seed    int   1997  random generator seed
       -vdwd   real  0.105  default vdwaals distance
      -shell   real      0  thickness of optional water layer around solute
     -maxsol    int      0  maximum number of solvent molecules to add if
                            they fit in the box. If zero (default) this is

Program genbox, VERSION 3.3.1
Source code file: statutil.c, line: 799

Invalid command line argument:

for the quiery in the first line. pls help me. i am using GROMACS in debian.

thanking you
umamaheswar reddy

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