[gmx-users] Invalid order for directive atomtypes

[afsaneh maleki]

Dear GMX users,

To generate a topology file for an arbitrary molecule (TP) on graphite
surface, I used g_x2top program to generate “TP.itp” file and I manually
construct "graphite.itp" file.

Generated topology file is as the following:

#include "./oplsaa.ff/forcefield.itp"

#include "TP.itp"

#include "graphite.itp"



[ system ]

TP ON GRAPHITE



[ molecules ]

;molecule name    nr.

TP        2

grap    6400



…….

And the graphite.itp is as the following:



 [ moleculetype ]

;  name  nrexcl

  grap       1



[ atoms ]

;   nr  type    resnr    residu   atom    cgnr     charge

   1   opls_145     1      grap     C       1      0.000



I run grompp for EM with this command line: grompp -f *.mdp –c *.gro -p
*.top -o *.tpr

It gave me the following error:

………

Fatal error:

Syntax error - File ffnonbonded.itp, line 1

Last line read:

'[ atomtypes ]'

Invalid order for directive atomtypes

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

…….

I know things in the [ molecules ] section need to line up with what's in
the  *.gro file.

Also I looked at that link but I don’t know how to solve this problem.

And other question is:

Do I need to make “nonbonding.itp” to insert in topology file for
introducing nonbonding interaction of graphite with TP molecule?



Sincerely

Afsaneh