[gmx-users] generating a top file

Yang Ye leafyoung at yahoo.com
Sun Jun 10 14:52:43 CEST 2007

This is called parameterization.

For small molecule, you can opt for PRODRG for GROMOS/GROMACS force 
fields; or Antechamber for AMBER force field.
Once you obtained the topology, convert them back to the format in the 
rtp file according to the manual.

Yang Ye

On 6/10/2007 7:28 PM, Shahrokh Safarian wrote:
> Dear colleagues
> As you know if we want to introduce a new molecule into Gromacs, the
> related parameters for that molecule (e.g. [atoms], [bonds], [pairs],
> [dihedrals] and so on) should be inserted to the Gromacs rtp file. In
> the Gromacs user's manual (page 100) an example for these types of
> topology parameters is propounded for urea molecule. The main question
> is how can we obtain these topology parameters for a desired molecule?
> regards
> saf
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