[root@localhost model2]# grompp -f em.mdp -c mod_b4em.pdb -p mod.top -o em.tpr
                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                            :-)  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.

                                :-)  grompp  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f         em.mdp  Input, Opt!  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c   mod_b4em.pdb  Input        Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -r       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
 -rb       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -n      index.ndx  Input, Opt.  Index file
-deshuf  deshuf.ndx  Output, Opt. Index file
  -p        mod.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o         em.tpr  Output       Generic run input: tpr tpb tpa xml
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj
  -e       ener.edr  Input, Opt.  Generic energy: edr ene

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
       -nice    int      0  Set the nicelevel
      -[no]v   bool    yes  Be loud and noisy
       -time   real     -1  Take frame at or first after this time.
         -np    int      1  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X coordinate
-[no]rmvsbds   bool    yes  Remove constant bonded interactions with virtual
                            sites
       -load string         Releative load capacity of each node on a
                            parallel machine. Be sure to use quotes around
                            the string, which should contain a number for
                            each node
    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals
  -[no]renum   bool    yes  Renumber atomtypes and minimize number of
                            atomtypes

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 44557
Excluding 1 bonded neighbours for Cl 1
NOTE:
  System has non-zero total charge: 1.400000e+01

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#      BONDS:   4099
#     ANGLES:   6012
#      PDIHS:   2084
#      IDIHS:   2209
#       LJ14:   7475
#     SETTLE:   44557
initialising group options...
processing index file...
Analysing residue names:
Opening library file aminoacids.dat
There are: 44558      OTHER residues
There are:   396    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 137679 elements
Making dummy/rest group for Acceleration containing 137679 elements
Making dummy/rest group for Freeze containing 137679 elements
Making dummy/rest group for Energy Mon. containing 137679 elements
Making dummy/rest group for VCM containing 137679 elements
Number of degrees of freedom in T-Coupling group rest is 279363.00
Making dummy/rest group for User1 containing 137679 elements
Making dummy/rest group for User2 containing 137679 elements
Making dummy/rest group for XTC containing 137679 elements
Making dummy/rest group for Or. Res. Fit containing 137679 elements
Making dummy/rest group for QMMM containing 137679 elements
T-Coupling       has 1 element(s): rest
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...

Back Off! I just backed up em.tpr to ./#em.tpr.2#

gcq#166992520: Thanx for Using GROMACS - Have a Nice Day

[root@localhost model2]#