[gmx-users] top file confusion

[Mark Abraham]

Rongliang Wu wrote:
> Hello gmx-users,
> 
> 	      the gromacs3.3 has an decane.itp file included in top folder, but the decane top i generated with pdb2gmx has somthing different. the function type of dihedrals for the former is 3 while the latter is 1, i don't know what a 3 type is for dihedrals. is it a mistake for the itp file enclosed?

There are sections in the manual that describe the various kinds of
dihedral functional forms, and others that describe the format of .rtp
and .itp files. Reading them will help enlighten you about how pdb2gmx
uses the default bonded interaction types for each force field to
generate the .top file.

Mark