joao@trial_joao: gmx grompp -f vacuum.mdp -c protein.gro -p topol.top -o protein_vac.tpr
GROMACS:    gmx grompp, VERSION 5.0.4

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Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
Peter Tieleman     Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

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check out http://www.gromacs.org for more information.

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GROMACS:      gmx grompp, VERSION 5.0.4
Executable:   /home/software/science/gromacs5/bin/gmx
Library dir:  /home/software/science/gromacs5/share/gromacs/top
Command line:
  gmx grompp -f vacuum.mdp -c protein.gro -p topol.top -o protein_vac.tpr

Setting the LD random seed to 4181414547
Generated 73900 of the 73920 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 47534 of the 73920 1-4 parameter combinations

ERROR 1 [file topol.top, line 1221]:
  No default U-B types


ERROR 2 [file topol.top, line 1222]:
  No default U-B types


ERROR 3 [file topol.top, line 1225]:
  No default U-B types


ERROR 4 [file topol.top, line 1683]:
  No default Proper Dih. types


ERROR 5 [file topol.top, line 1684]:
  No default Proper Dih. types


ERROR 6 [file topol.top, line 1685]:
  No default Proper Dih. types


ERROR 7 [file topol.top, line 1686]:
  No default Proper Dih. types


ERROR 8 [file topol.top, line 1687]:
  No default Proper Dih. types


ERROR 9 [file topol.top, line 1688]:
  No default Proper Dih. types


ERROR 10 [file topol.top, line 1689]:
  No default Proper Dih. types


ERROR 11 [file topol.top, line 1690]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein'

NOTE 1 [file topol.top, line 2436]:
  System has non-zero total charge: 3.000000
  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.




ERROR 12 [file topol.top, line 2436]:
  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.


Removing all charge groups because cutoff-scheme=Verlet

There was 1 note

-------------------------------------------------------
Program gmx, VERSION 5.0.4
Source code file: /home/software/science/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 1723

Fatal error:
There were 12 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------