When runnning a minimization invoking Tinker9 minimize with an organic molecule parametrized with OPLS (Ligpargen command-line v.2.1), I notice aromatic rings warped when the molecule is zwitterionic, like the following one...
So the result is this:
I´ve checked the .key file, comparing it with other non-zwitterionic molecules, and the parametrisation looks fine. Aromatic atoms are accordingly labelled with CA atom types, torsional values ok, etc. I haven´t escrutinize the file carefully, just a superficial check. LigParGen paraetrisation was run with the following arguments:
Hi,
When runnning a minimization invoking Tinker9 minimize with an organic molecule parametrized with OPLS (Ligpargen command-line v.2.1), I notice aromatic rings warped when the molecule is zwitterionic, like the following one...
So the result is this:
I´ve checked the .key file, comparing it with other non-zwitterionic molecules, and the parametrisation looks fine. Aromatic atoms are accordingly labelled with CA atom types, torsional values ok, etc. I haven´t escrutinize the file carefully, just a superficial check. LigParGen paraetrisation was run with the following arguments:
ligpargen -i mol.pdb -r MOL -c 1 -o 0 -n mol -cgen CM1A
So I´m wondering either this is an artifact of the parametrisation
or either
an issue of the oplsa-aa force field contained in tinker. I would appreciate any ideas in regards to this.
Thank you kindly,
E77.