Desmond to gromacs nrexcl 0 warning

[sirishkaushik]

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:

 1 N1                    141 PHE      N1            0        -0.30000000        14.00670000
 2 C1                    141 PHE      C2            1         0.25000000        12.01115000
 3 C2                    141 PHE      C3            2         0.50000000        12.01115000

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