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:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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