Re: Parameter and Topology Question - New NA Residues
12/02/22 07:36 PM
NAMD != CHARMM, so you might get some useful feedback by using a different program
Since the fragments are all biomolecules well represented in the force fields, the best strategy is to use CCGenFF (or FFparam) just for the sugar-amino acid linkage using a simple model fragment, and use existing parameters for the most part. I probably would not use charmm-gui for this.
I guess you don't plan to publish the work or continue in the field, if a rough simulation is good enough.