I'm currently working on membrane protein dockings, and I'm trying to prepare a file for molecular dynamics in NAMD, unfortunatelly after i try to combine the protein and membrane files, VMD thinks that there are covalent bonds between membrane lipids and my protein. I'm guessing it's because the lipis and protein are in close distance to each other. Did anyone have this problem, and knows a solution?
Justin Lemkul
What VMD thinks are bonds and what are actually defined as bonds in the PSF are independent. VMD guesses what bonds on purely based on distances. Only the PSF matters for the actual simulation. Perhaps there are some close contacts, but they should be resolved using energy minimization.
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