[gmx-users] GROMACS_reverse version command g_fg2cg

francesca vitalini francesca.vitalini11 at gmail.com
Thu Jan 26 17:17:39 CET 2012


I'm a new GROMACS user and I'm trying to convert a CG file (I have the .top
and .gro for it) to AA using the reverse command g_fg2cg.

Unfortunately I don't have the AA topology file, only the pdb, so I'm
trying to get one using pdb2gmx genbox and genion subsequently. Then I try
to run the g_fg2cg command and what I get is an error message

Fatal error:

Atoms in the .top are not numbered consecutively from 1

I have checked the FG .top file and actually found that the residues were
not named from one, so I changed it and tried again but with the same
result. In my system I have a dimer plus water plus ions so I thought that
the problem might have occurred because in the .itp files for each monomer
the residue numeration was starting from 1; not knowing if it could cause
the problem I tried to re-numerate the residues in the second .itp file in
order to match with those of the first file but with no change in the

I’ve read on the web that with grompp a similar error message was found and
it was due to the presence of ions after solvent so I tried to change the
order of the ion.itp file in the topology but it didn’t change anything.

I post here the whole error message, hoping that it can be useful.

Option     Filename  Type         Description


-pfg dynamin_dimer_fg.top  Input        Topology file

-pcg dynamin_dimer_cg.top  Input, Opt!  Topology file

  -c dyn_dimer_cg.gro  Input        Generic trajectory: xtc trr trj gro g96


  -o dynamin_dimer_fg_random.groq.gro  Output       Generic structure: gro

                                   g96 pdb xml

      Option   Type  Value  Description


      -[no]h   bool     no  Print help info and quit

       -nice    int      0  Set the nicelevel

          -n    int      0  1: fg2cg transformation, 0: cg2fg transformation

        -wat    int      0  1: rewrites FG_CG water to true fg water;

        -rad   real    0.3  A radius for random atom insertion;

calling cpp...

dynamin_dimer_fg.top:38:2: error: invalid preprocessing directive #;

dynamin_dimer_fg.top:51:2: error: invalid preprocessing directive #SOL

cpp exit code: 256

Tried to execute: 'cpp
dynamin_dimer_fg.top > gromppqBsIeH'

The 'cpp' command is defined in the .mdp file

processing topology...

Generated 165 of the 1596 non-bonded parameter combinations

Cleaning up temporary file gromppqBsIeH


Program g_fg2cg, VERSION 3.3.1

Source code file: ../kernel/toppush.c, line: 758

Fatal error:

Atoms in the .top are not numbered consecutively from 1

Hope you can help me with that.

Many Thanks

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