[gmx-users] NO such a molecule type

[Mark Abraham]

Morteza Khabiri wrote:
> Dear Mark,
> 
> Thanks for your help. As you said I define cpp path for my system. Now I
> get 1 warning and the following error. To be mor clear, I also paste my
> mdp file.

OK, but it's the .top file that is pertinent now.

> checking input for internal consistency...
> WARNING 1 [file md_bfgs.mdp, line unknown]:
>   Removing the rotation around the center of mass in a periodic system
>   (this is not a problem when you have only one molecule).
> calling /lib/cpp...
> processing topology...
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Cleaning up temporary file gromppDFgrVF
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: topio.c, line: 389
> 
> Fatal error:
> Invalid order for directive defaults, file
> ""/usr/local/gromacs/share/top/ffoplsaa.itp"", line 18

You're mangling your .top file, either with a misordered or extra 
#include to your forcefield file.

Mark