Hi everyone
I'm new in all the field of molecular dynamics, but i trying to run a SMD of one protein with two isopeptide bond, one in each domain, that prevent my protein stretch.
My problem is that, i dont know how to include my isopeptide bond in my emdrun, beacause when i minimize, the bond doesn't stay in the protein and i need those bonds to measure the force and to run the SMD.
Can someone help me?
I atach the pdb of my protein.
Hi,
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf
Hey Tomas,
I know I'm late to the party, but you need to use a force field that is designed to recognise and accept isopeptide bonds such as Forcefield_PTM - modifying a force field for your specific purposes is rather difficult, so it is best to try to find some publication that uses MDS with the same PTM that you are interested in and contact the author about which force field they used and if you may use it too if they modified it.
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