From: Vermaas, Joshua (
Date: Wed Oct 16 2019 - 14:10:10 CDT

Hi Paula,

The only thing that the ssrestraints plugin does is to generate an extrabonds file that adds extra harmonic restraints to enforce the secondary structure present in the original protein/nucleic acid system. If you want to enforce secondary structure onto something else, you'd need to know what the key features are for your secondary structure and make a similar text file to feed into NAMD's input deck. For instance, for alpha-helices, one of the key features is the hydrogen bonding between the ith and i+4th residue, and this is one of the interactions that ssrestraints strengthens.


On 2019-10-16 12:24:13-06:00 wrote:


How can I apply SS restraints on a non-protein/nucleic segments of the system for MDFF?