[gmx-users] Invalid order for directive atomtypes
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
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
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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