VMD-L Mailing List

From: SHIVAM TIWARI (t.shivam_at_iitg.ac.in)
Date: Sun Jan 31 2021 - 06:22:14 CST

Dear all,
This is regarding topology tutorial, a particular line is like this

"bonding an O atom to CG would require choosing a type for the O atom, which is impossible, since there is no topology entry with O bonded to a proline or proline-like ring. We simply do not have parameters for oxygen bonded to a 5-member proline ring."

This brings a question in my mind that, how one will know a priori whether a particular topology exist in CHARMM or not, ok the above case is a simple one, in a way that it belongs to the standard amino acid. But, what if my molecule, let us say contains some parts which are not amino acids. How do I search all the existing topological information in CHARMM force field and not just protein topology.

regards
shivam