jonathan@jonathan-desktop:~/Documents/gromacs_files/biotin_avidin_md$ grompp -f em.mdp -c rebuilt_system.gro -p system.top -o em.tpr
                         :-)  G  R  O  M  A  C  S  (-:

                      GROwing Monsters And Cloning Shrimps

                            :-)  VERSION 4.5.5  (-:

        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  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f         em.mdp  Input        grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c rebuilt_system.gro  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     system.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o         em.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.3#
Generated 2926 of the 2926 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2926 of the 2926 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 3 bonded neighbours molecule type 'biotin'

NOTE 1 [file system.top, line 54]:
  System has non-zero total charge: -4.000021
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
  


Analysing residue names:
There are:   480    Protein residues
There are: 15568      Water residues
There are:    10      Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 161946.00
Largest charge group radii for Van der Waals: 2.982, 2.377 nm
Largest charge group radii for Coulomb:       3.734, 3.329 nm

WARNING 1 [file em.mdp]:
  The sum of the two largest charge group radii (7.062195) is larger than
  rlist (1.000000)


Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.111 0.111 0.111
Estimate for the relative computational load of the PME mesh part: 0.26

NOTE 2 [file em.mdp]:
  This run will generate roughly 3125 Mb of data


There were 2 notes

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 1603

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

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