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<FONT FACE="Lucida Grande"><SPAN STYLE='font-size:11pt'>Hello all. Just a quick clarification, please.<BR>
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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.<BR>
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Now my questions. <BR>
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Prodrg4.5beta produces .itp files for all my ligands where under the [moleculetype] section it states that nrexcl is 3. <BR>
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Doesn’t this automatically exclude all (1-4) interactions for that ligand? <BR>
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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?<BR>
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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? <BR>
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Doesn’t this imply that the default for ffG53a6 intra-molecular protein-atom/protein-atom non-bonded interactions is nrexcl =2 ?<BR>
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Thanks in advance for any clarification in this area. I just want to be sure I’m accounting for my exclusions properly.<BR>
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Regards,<BR>
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Dean<BR>
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"It was pretty good. Even the music was nice."<BR>
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Yogi Berra, after attending an opera<BR>
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