[gmx-users] Invalid order for directive atomtypes

[Justin Lemkul]

On 8/23/13 3:29 AM, afsaneh maleki wrote:
> 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.
>

True, but not relevant in this case - grompp never gets past the initial stages 
of parsing the force field, let alone the system-level information.

> 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?
>

No, but apparently something is screwed up in the parent force field.  Are you 
introducing new atom types in either of your molecule .itp files?  It seems that 
grompp is complaining about the formatting of one of the force field files, 
though - have you altered them in any way?  Is there any reason you need a local 
version of OPLS-AA?  Does #including the original OPLS-AA force field instead of 
the local one fix the issue?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================