This is called parameterization.
http://wiki.gromacs.org/index.php/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.
Regards,
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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