Repelling extracellular regions of the protein from membrane in NAMD MD simulation

From: Sahu, Indra (
Date: Sat Feb 09 2013 - 14:58:24 CST

Hi All,
I am trying to do NAMD MD simulation on a membrane protein (pdb id:2k21) in
POPC lipid bilayers. I am following the membrane protein tutorials provided
in NAMD website. My protein has 129 amino acids with a single trans
membrane domain (45-71)and extra cellular regions at both C- and
N-terminals. The solution NMR structure of this protein has spherical
shape. While setting up the simulation system, I put the protein inside a
patch of POPC lipid and removed the overlapping lipids in VMD. Since the
shape of protein is spherical, I couldn't move the extra cellular region
from the interior membrane. After running the MD simulation for energy
minimization and final production run for 50 ns. The extracellular regions
still remain inside the membrane interior. I think there would be a way to
repel the C-terminal and N-terminal extracellular regions. It would be
great if any one could help to fix the issue.

Indra Dev Sahu, PhD
Chemistry and Biochemistry Department
Miami University, Oxford, OH

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