[gmx-users] Custom elastic network of a membrane protein

[Yasser Almeida Hernández]

Hi all,

I am simulating a membrane protein in DPPC in order to insert it in the 
bilayer. I did a previous run during 2 us and I saw major changes in the 
secondary structure. Now I want to use an elastic network in order to 
preserve the overall secondary structure.

It is possible to build an elastic network, lets say the TM helices, 
excluding other parts of the protein, ej. soluble domains, with 
martinize.py (or any other tool)?

Thanks

Yasser

-- 
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c