[gmx-users] Assigning OPLS-AA atom types to new ligands

Shang-Te Danny Hsu hsu at nmr.chem.uu.nl
Fri Apr 1 18:35:03 CEST 2005

It is a general question of the use of OPLS-AA force field.

I would like to assign OPLS-AA atom types, which are a few hundreds, to 
atoms in residues that are not defined in the GROMACS library. Unlike 
GROMOS, which has only 45 atom types, it is not trivial to me as to how 
one can decide which atom type is to be assigned to a certain chemical 
group, although each atom type has a simple description.

For instance, how can I create a GROMACS topology file of a 
N-acetyl-glucoseamine (GlcNAc) with OPLS-AA atom types?

I failed to find a manual for OPLS-AA describing a general procedure of 
such assigning process. Can someone explain or direct me to resolve this 

Thanks, Danny

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