[gmx-users] Inserting protein in Bilayer

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 11 22:30:32 CEST 2009

sunny mishra wrote:
> Hi All,
> I am working on the CG simulations of the proteins and lipid bilayers.
> I am confused of how to set up the whole system for simulations. I got
> the DSPC lipid bilayer from martini website and I have 1SU4.pdb file
> with me. I cleaned the .pdb file and now I want to include the 14 DSPC
> molecules in my .pdb file. I don't know if I am going in the right
> direction or not. Please let me know how to set up the simulation for
> the same if you have some idea. I will appreciate your help.

I wrote a tutorial for atomistic membrane protein systems:


It may provide some useful information, since the premise for constructing the 
system is the same.  Our web server is currently down due to a power outage at 
our University, but I should have everything up and running by tomorrow.


> Thanks,
> Suny
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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