VMD-L Mailing List
From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Oct 16 2019 - 14:10:10 CDT
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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.
-Josh
On 2019-10-16 12:24:13-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
Hi!
How can I apply SS restraints on a non-protein/nucleic segments of the system for MDFF?
Thanks
Paula
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