[gmx-users] Invalid order for directive atomtypes
maleki.afsaneh at gmail.com
Fri Aug 23 09:29:24 CEST 2013
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:
[ system ]
TP ON GRAPHITE
[ molecules ]
;molecule name nr.
And the graphite.itp is as the following:
[ moleculetype ]
; name nrexcl
[ 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:
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?
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