undergrad j wrote:
Hello there!
I am an undergraduate working on my thesis, which involves the
simulation of a DPPC membrane. My college is small and the department
does not have experience with MD simulations, so I am 100% on my own. I
have successfully modeled simple proteins in water- but I want to move
onto bilayers.
I am attempting to simulate a simple, homogeneous DPPC bilayer. I have a
.pdb file of the membrane, along with .itp files provided by
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I
am following this procedure for setting up the membrane:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html
However, I feel like I am missing something? The procedure is telling me
to alter a .top file to accommodate the altered force field .itp's
(ffG53a6 to include Berger lipid parameters-which I have already
accomplished)- maybe the .top in question is the topology of the protein
that is being implanted in the membrane? I do not want a membrane bound
protein in this simulation- so how do I generate a .top for a simple
membrane? Is it through pdb2gmx? Do I have to manually program the
system topology?
Maybe someone can point me to a detailed procedure for setting up a
simple membrane system from start to finish...?
A suitable topology for a DPPC-only system is provided as part of my tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/topol_dppc.top
It's rather simple and does not require pdb2gmx, just the extended 53a6 force
field. If you've already got that, you're just about done.
-Justin
I am probably going to be bugging this group a lot in the next few
weeks- thank you for reading this....
(Sorry if this question is confusing/sounds silly- again, I'm working on
my own)
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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