From: sunyeping (sunyeping_at_aliyun.com)
Date: Wed Oct 08 2014 - 21:58:02 CDT
Maybe you should check the reasonality of your initial structure, including improper atom positions, bond angle, and dihedral angles, ect..
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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发件人：Cuong Nguyen <cuong1972_at_gmail.com>
发送时间：2014年10月9日(星期四) 09:37
收件人：tutorial-l <tutorial-l_at_ks.uiuc.edu>
主 题：tutorial-l: Protein structure distorted after Energy minimization with NAMD
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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