Re:tutorial-l: Protein structure distorted after Energy minimization with NAMD

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 ------------------------------------------------------------------ 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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