Re: Membrane protein simulaton

From: Eduard Schreiner (
Date: Fri Jan 14 2011 - 19:08:43 CST

There is a tutorial dealing with setting up a membrane-protein system
which will answer your questions if you work through it. Check
"Membrane Proteins Tutorial"


On Fri, Jan 14, 2011 at 6:19 PM, snoze pa <> wrote:
> Dear NAMD users,
> I am trying to setup a NAMD simulation for membrane protein. I have a
> question related to setup?
> 1. I have to remove part of the lipid that is in contact with protein.
> I am not sure how much of the lapid molecule I should cut? shall I
> remove with in 0.6A from protein?
> 2. How can I avoid water from entering into membrene during
> simulation. I found a script keep_water_out.tcl in NAMD tutorial but I
> don't know how to use it.
> I will highly appreciate your help solving this protein.
> Thanks in advance.
> S

Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078

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