[gmx-users] Invalid order for directive atomtypes

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Aug 4 09:10:59 CEST 2013

Hi Jonathan,

The itp's for the ligands were given atomtype sections, but atomtypes (and
other *types) may only be defined before any moleculetype definition (check
chapter 5 of the manual for the topology format). You'll need to remove
anything before the moleculetype directive from the itp files and make sure
that all the atomtypes (and other *types) referred to are correct according
to the listing in the force field.

Hope it helps,


On Sun, Aug 4, 2013 at 8:46 AM, Jonathan Saboury <jsabou1 at gmail.com> wrote:

> PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2
> Commands used: http://pastebin.com/raw.php?i=YYG5ad7A
> Compressed folder containing all files (10.2 MB):
> http://www.sendspace.com/file/rka8ei
> So I want to simulate this complex. I am having problems with the .itp's
> and do not know why.
> I get the error:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/topio.c, line: 656
> Fatal error:
> Syntax error - File NAG_GMX.itp, line 3
> Last line read:
> '[ atomtypes ]'
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Here is the logic I used while trying to get teh simulation to work, please
> let me know if this is correct, because there wasn't a tutorial example
> like this.
> 1.) Separate the complexed pdb into teh standard residues and ligands, so
> "ATOM", "HEM", "NAG" and "S58"in this case.
> 2.) There are multiple ligands in the pdb, so I need to delete all but one
> molecule and create a forcefield .itp so I can include it in the .top file.
> 3.) Once the .itp's for the single molecules are created, you need to put
> the complex back together. I was having problems with adding charges, so I
> only added hydrogen’s to the ligands and created complex.pdb from the new
> pdb files created from acpype.
> 4.) Minimize, relax waters, then simulate.
> So what did I do wrong here? Thanks!! :)
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Tsjerk A. Wassenaar, Ph.D.

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