[gmx-users] Invalid order for directive atomtypes

[Mark Abraham]

On Fri, Jul 4, 2014 at 6:32 PM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>
> I generate a ligand .itp file by acpype based on gaff FF. I included it in
> topol.top as following:
>
> ; Include forcefield parameters
> #include "amber99sb-star-ildn.ff/forcefield.itp"
> #include "protein.itp"
> #include "ligand.itp"
>
> when I try to run grompp, it always failed with messages:
>
>
> Fatal error:
> Syntax error - File ligand.itp, line 3
> 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 google the old thread, it said we should change the order of itp, but put
> ligand.itp on the first line, but the problem is still there.


A different problem can happen; the same problem can't. But we don't know
what the messages were, or the link you followed, so we're stuck. Perhaps
you can learn about directive order in 5.7.1 of the manual - you cannot
ever have [atomtypes] after [molecules], even if they're in .itp files.

Mark


> Here is
> initial lines for ligand.itp:
>
>
> [ atomtypes ]
> ;name   bond_type     mass     charge   ptype   sigma         epsilon
> Amb
>  na       na          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ;
> 1.82  0.1700
>  ca       ca          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ;
> 1.91  0.0860
>  cc       cc          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ;
> 1.91  0.0860
>  nd       nd          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ;
> 1.82  0.1700
>  cd       cd          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ;
> 1.91  0.0860
>  cl       cl          0.00000  0.00000   A     3.47094e-01   1.10876e+00 ;
> 1.95  0.2650
>  ne       ne          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ;
> 1.82  0.1700
>  hn       hn          0.00000  0.00000   A     1.06908e-01   6.56888e-02 ;
> 0.60  0.0157
>  nh       nh          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ;
> 1.82  0.1700
>  c3       c3          0.00000  0.00000   A     3.39967e-01   4.57730e-01 ;
> 1.91  0.1094
>  f        f           0.00000  0.00000   A     3.11815e-01   2.55224e-01 ;
> 1.75  0.0610
>  ha       ha          0.00000  0.00000   A     2.59964e-01   6.27600e-02 ;
> 1.46  0.0150
>  h1       h1          0.00000  0.00000   A     2.47135e-01   6.56888e-02 ;
> 1.39  0.0157
>  sy       sy          0.00000  0.00000   A     3.56359e-01   1.04600e+00 ;
> 2.00  0.2500
>  o        o           0.00000  0.00000   A     2.95992e-01   8.78640e-01 ;
> 1.66  0.2100
>  n4       n4          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ;
> 1.82  0.1700
>  hx       hx          0.00000  0.00000   A     1.95998e-01   6.56888e-02 ;
> 1.10  0.0157
>  hc       hc          0.00000  0.00000   A     2.64953e-01   6.56888e-02 ;
> 1.49  0.0157
>  oh       oh          0.00000  0.00000   A     3.06647e-01   8.80314e-01 ;
> 1.72  0.2104
>  ho       ho          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ;
> 0.00  0.0000
>
>
>
> Does anybody have any idea?
>
> thx a lot
> --
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