[gmx-users] prodrg 4.5beta generated topologies and exclusions
Mark.Abraham at anu.edu.au
Mon Jun 15 14:45:21 CEST 2009
Dean Cue bas wrote:
> 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.
> Doesn’t this automatically exclude all (1-4) interactions for that ligand?
Yes, such interactions are excluded.
> If so, then doesn’t that automatically negate the need to explicitly
> exclude the (1-4) interactions for planar aromatic systems as described
> above in the ff paper?
The authors of that paper were probably not pre-supposing the use of any
particular topology-generation tool.
> If so, then doesn’t 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 ligands?
It would seem so. If this bothered me, I would start by reading the
PRODRG documentation - but I would have done that before using anything
> Doesn’t this imply that the default for ffG53a6 intra-molecular
> protein-atom/protein-atom non-bonded interactions is nrexcl =2 ?
That might depend on the mechanism that is being used for the different
and/or missing 1-4 interactions. Pre-excluding and then adding might be
easier than pre-including and then excluding.
> Thanks in advance for any clarification in this area. I just want to be
> sure I’m accounting for my exclusions properly.
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