[gmx-users] help about topol.tpr file of small molecular complex

[Christoph Freudenberger]

You should consider using quantum chemistry to deal with
that kind of problem.
Check out programs like Spartan, Titan or Gaussian.

Rongjian Sa wrote:
> Dear everyone:
> I want to use gromacs to simulate the interaction between two molecules. 
> My system contain one ammonium and one benzene molecules. I have only 
> obtain one benzene molecule. I have attached my pdb file. So I want to 
> know who can help me about this.
>  
> Sincerely yours,
> Rongjian
>  
> PDBFIL pdb file created from cpmd Wannier file: ELF
> ATOM      1 C    MOL     1      -0.001   0.620   1.405  1.00 10.00
> ATOM      1 C    MOL     1       1.214   0.616   0.703  1.00 10.00
> ATOM      1 C    MOL     1       1.214   0.615  -0.702  1.00 10.00
> ATOM      1 C    MOL     1      -0.001   0.618  -1.404  1.00 10.00
> ATOM      1 C    MOL     1      -1.215   0.623  -0.702  1.00 10.00
> ATOM      1 C    MOL     1      -1.215   0.625   0.703  1.00 10.00
> ATOM      2 H    MOL     1       0.000   0.643   2.494  1.00 10.00
> ATOM      2 H    MOL     1       2.158   0.641   1.247  1.00 10.00
> ATOM      2 H    MOL     1       2.158   0.639  -1.247  1.00 10.00
> ATOM      2 H    MOL     1       0.000   0.639  -2.493  1.00 10.00
> ATOM      2 H    MOL     1      -2.159   0.655  -1.247  1.00 10.00
> ATOM      2 H    MOL     1      -2.159   0.657   1.247  1.00 10.00
> ATOM      2 H    MOL     1       0.009  -2.971   0.845  1.00 10.00
> ATOM      2 H    MOL     1       0.009  -2.975  -0.847  1.00 10.00
> ATOM      2 H    MOL     1      -0.833  -1.757  -0.003  1.00 10.00
> ATOM      2 H    MOL     1       0.821  -1.735  -0.003  1.00 10.00
> ATOM      3 N    MOL     1       0.002  -2.382  -0.002  1.00 10.00

-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785