From: Cuong Nguyen (
Date: Wed Oct 08 2014 - 20:37:26 CDT

Hello NAMD Users:

I am a new user of NAMD. I followed the instructions in the NAMD tutorial
to run energy minimization for my protein with NAMD. After minimization
step, my protein structure distorted a lot, beta strands to coils. My
protein was generated from homology modeling with multiple templates having
sequence identity ranging from 35-40%.

Is there any way in NAMD to fix secondary structure before running energy
minimization or dynamic simulation?

I appreciate your help on this.

Cuong Nguyen

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