[gmx-users] OPLSAA parameters

[Mark Abraham]

friendli wrote:
> In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type 
> opls_235 and opls_236.
> While in oplsaanb.itp, the atom type opls_235 and opls_236 corresponds 
> to atom "name"(as display in titles in oplsaanb.itp) C and O.
> 
> why there are two different "name"s for the same atom? what is the 
> difference?

Different force fields use the machinery differently, but I can't think 
of a purpose for the atom name field in the parameter .itp file if there 
is a separate atom type.

The purpose of atom names, residue names and residue numbering in a 
pre-pdb2gmx structure file is to look up the right atom types in the 
.rtp file and write them to the .top file. The purpose of the atom types 
in the .top file is to look up the right parameters in the .itp file 
when running grompp. At that point, atom names are probably just for 
user convenience.

Mark