[gmx-users] prodrg 4.5beta generated topologies and exclusions

Dean Cuebas deancuebas at missouristate.edu
Sun Jun 14 05:10:29 CEST 2009

Hello all. Just a quick clarification, please.

Reading the original GROMOS53A6 paper, it appears that 2nd neighbor (1-3)
interactions are always excluded, and that third neighbor (1-4) non-bonding
interactions are used, yet modified in some circumstances. The paper also
states that all (1-4) interactions should be explicitly excluded for atoms
either within or directly bonded to aromatic rings to help keep planarity. I
could confirm this in the adenine topology in the ffG53a6.rtp file where
there were the above described exclusions in the [exclusions] section for
that residue.

Now my questions. 

Prodrg4.5beta produces .itp files for all my ligands where under the
[moleculetype] section it states that nrexcl is 3.

Doesn¹t this automatically exclude all (1-4) interactions for that ligand?

If so, then doesn¹t that automatically negate the need to explicitly exclude
the (1-4) interactions for planar aromatic systems as described above in the
ff paper?

If so, then doesn¹t excluding all these third neighbor (1-4) interactions
for ligand topologies produced by Prodrg ignore intra-molecular interactions
that are important in the simulated behavior and properties of these

Doesn¹t this imply that the default for ffG53a6 intra-molecular
protein-atom/protein-atom non-bonded interactions is nrexcl =2 ?

Thanks in advance for any clarification in this area.  I just want to be
sure I¹m accounting for my exclusions properly.




"It was pretty good. Even the music was nice."

Yogi Berra, after attending an opera

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