[gmx-users] help about topol.tpr file of small molecular complex
Rongjian Sa
rjsa at mail.shcnc.ac.cn
Tue Jun 3 10:22:00 CEST 2003
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
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