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 ligands? 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. Regards, Dean "It was pretty good. Even the music was nice." Yogi Berra, after attending an opera
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php