[gmx-users] Odd error

[David van der Spoel]

Christopher Stiles wrote:
> 
> 
> I have been using Gromacs for some time now and actually today I have 
> been using it without a problem but then all a sudden commands that I 
> had been using stopped functioning properly. The following is an example 
> of this:
> 
>  
> 
> ############################################
> 
>  
> 
> -bash-3.00$ genbox -cp SWNT_6_6_144.gro -cs -o SWNT_6_6_144_b4em.gro -p 
> SWNT_6_6
> 
> _144.top -maxsol 804
> 
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>  
> 
>                    Good gRace! Old Maple Actually Chews Slate
> 
>  
> 
>                             :-)  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 SWNT_6_6_144.gro -cs.gro  Input, Opt!  Generic structure: gro g96 pdb
> 
>                                    tpr tpb tpa xml
> 
>  -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
> 
>                                    xml
> 
>   -o SWNT_6_6_144_b4em.gro  Output       Generic structure: gro g96 pdb xml
> 
>   -p SWNT_6_6_144.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    804  maximum number of solvent molecules to add if
> 
>                             they fit in the box. If zero (default) this is
> 
>                             ignored
> 
>  
> 
> WARNING: masses will be determined based on residue and atom names,
> 
>          this can deviate from the real mass of the atom type
> 
> In case you use free energy of solvation predictions:
> 
>  
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> 
> D. Eisenberg and A. D. McLachlan
> 
> Solvation energy in protein folding and binding
> 
> Nature 319 (1986) pp. 199-203
> 
> -------- -------- --- Thank You --- -------- --------
> 
>  
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
> 
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> 
> -------------------------------------------------------
> 
> Program genbox, VERSION 3.3.1
> 
> Source code file: futil.c, line: 340
> 
>  
> 
> File input/output error:
> 
> SWNT_6_6_144.gro -cs.gro
> 
> -------------------------------------------------------
> 
>  
> 
> "I Live the Life They Wish They Did" (Tricky)
> 
>  
> 
> ##############################################
> 
>  
> 
> Has any one else experience such a problem? This is not limited to just 
> this one command, it seams that it is now not reading the commands 
> properly. I have restarted the server in an vain hopes it would fix its 
> self but this has had no effect.

it can't find the file. you may have mistyped its name are added a space 
in the middle.
> 
>  
> 
> Thank you,
> 
> ~Christopher Stiles
> 
> College of Nanoscale Science and Engineering (CNSE)
> 
> State University of New York , Albany , New York 12203 , USA
> 
>  
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se