[gmx-users] generating a top file

[Mark Abraham]

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.

Strictly, no. Only if you want pdb2gmx to recognise these new residue / 
molecule types do you need an .rtp entry. Otherwise your new parameters 
should go into a molecule .itp file and be #included in your .top file. 
See http://wiki.gromacs.org/index.php/Topology_File

Mark