Dear users,
In NCAA tutorial, in order to use molfile_to_params_polymer.py script, we have to update the mol file by adding some additional data at the end of mol file.
Actually I understand most of these additional data except the meanings of POLY_UPPER and POLY_LOWER: they are atom number for capping groups connecting to the residue. However, I donot understand the UPPER and LOWER meanings in these two terms. They are connected to C-ter and N-ter of the residue, but is there any relationship between "UPPER & LOWER" and "C-ter & N-ter" of the residue?
Thanks!
Category:
Post Situation:
The POLY_UPPER and POLY_LOWER atoms are those atoms which represent the connection points to the residue. If you think about the generated ResidueType which the new params file represents, it has polymeric connection points which tell it where the residues it's connected to on each end are. To help molfile_to_params_polymer.py figure out where those connection points should be and what sort of geometry it has, the POLY_LOWER atom is specified as the atom which represents the atom in the other residue which is connected to the N-terminal end of this residue. Likewise with the POLY_UPPER atom and the C-terminal connection point. The UPPER/LOWER refers to the direction of the polymeric chain. "Upper" means higher numerically in the chain (i.e. C-terminally), and "Lower" means lower numerically (i.e. N-terminally) - both are from the perspective of the current residue.
@rmoretti
Thank you very much for your kind reply.
Your explanation is very clear and thorough. I really appreciate it. Thanks!