I am trying to create the topology of a Metalloprotein that contains copper as an essential cofactor. However, it is giving errors, in crystals and modeled structures. I'm very new to the DM field and I'm trying to learn it myself. Can someone help me? Below is the link with PDB of a my protein, and a crystal (other protein) which is already adequate for copper loads
https://drive.google.com/drive/folders/111LiJ85JgGCcPL2Z_WkmrAqp2DSrfjrq
Handling metal ion is tricky in MD simulation, one possible approach is to link /convert the coordinate covalent bond of Cu ion to covalent bond, re-calculate the charges of interacting atoms/residues and create new amino acids reflecting the presence of Cu+, add them to amino acid library of force field.
The better thing is to look for someone who already publish the parameters of this set up. It will be lot easier for you to work with already tested parameters.
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