I am trying simulate interaction of a blood coagulation factor (a glycoprotein) with lipid bilayer using gromacs. As I know I have to parameterize glycan. But I don't know how to do that, Is any one help me?
Hi Fahimeh
It might somehow help, follow the links: http://www.cell.com/cms/attachment/597225/4675357/mmc1.pdf
http://scholarworks.sjsu.edu/cgi/viewcontent.cgi?article=1283&context=etd_projects
http://pubs.acs.org/doi/abs/10.1021/ct700324x
There is a web page that generates a topology file for molecules as well as protein: https://atb.uq.edu.au/index.py
If you calculate solvation free energy of you protein that gives the most reliable parameters!
Follow the tutorials
There are many tools and servers for parameterize use those
Use charmm forcefield and get help from CHARMM GUI might help. You might need some modifications to make it work
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