[gmx-users] Odd error

[Christopher Stiles]

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.

 

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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