We already have a section of exclusions where atoms less than 3 bonds away are included. Is there a specific reason to print this section again with only these three entries?
If this is confirmed to be redundant, I can proceed with manually removing this from the topology, but just wanted the users'/community's feedback before doing so.
Hi,
When I convert a Desmond CMS to gro using InterMol, the following lines are added to the topology:
[ exclusions ] 1 2 1 3 2 3
When this .top is subsequently read into OpenMM using GmxSimulation class, we get a warning:
"GromacsWarning: nrexcl 0 not currently supported"
Is there a reason InterMol adds these additional exclusion listings? if we go by atom-numbers, 1,2 3 are atoms from a Phe residue:
We already have a section of exclusions where atoms less than 3 bonds away are included. Is there a specific reason to print this section again with only these three entries?
If this is confirmed to be redundant, I can proceed with manually removing this from the topology, but just wanted the users'/community's feedback before doing so.
Thanks, Kaushik