[gmx-users] Invalid order for directive atomtypes

Jonathan Saboury jsabou1 at gmail.com
Sun Aug 4 08:46:37 CEST 2013

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):

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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