I need to construct a mixed lipid bilayer for simulating a membrane protein. I am trying in GROMACS, but I have a problem in orientation of protein in lipid mixed type lipid bilayer.
You can follow the following tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
It's also good to use structures of membrane proteins from OPM (http://opm.phar.umich.edu), since they're already properly oriented in the membrane.
Dear Bipin Singh,earlier I have follow that tutorial but their command given (gmx editconf -f protein.gro -o protein_newbox.gro -box (membrane box vectors) -center x y z)
i calculated box vector of membrane but i want to orient the protein in membrane according to protein hydrophobic region which are in a bottom of protein structure not in a middle part of protein.
If u know, plzzz tell me as soon as possible.
Dear Bartosz Trzaskowski ,
Thank u for your reply...
In OPM database, lots of protein is properly oriented but their not given a x y z of protein center, their only given hydrophobic thickness of membrane a/c to protein.
Below i have attached a image of protein oriented in membrane taken from OPM database. If i orient manually this protein through center of box vector of membrane and protein, protein are not orienting in membrane like OPM orientation .
For that i want to define (center x y z) of protein in gromacs for orient protein in membrane but i haven,t understand how do i calculate it??
Command line of gromacs
gmx editconf -f protein.gro -o protein1..gro -box 5.23840 13.47850 7.59650 -center x y z ??????
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