Hi dear All! Good day dear forum! I have a question abour freezing of atoms during MD. The idea is that - I have a protein and one domain contains a site. Also I have two ligands, one of them is better inhibitor in comparison with another one. To prepare the topology of the inhibitor I need to use a R.E.D.III server. As there are several different fitting methods, so I have to carry out a series of short MDs (about 5-10 ns) for each of them. The question is - is it possible to isolate this domain and fix/freeze last residues of the hairpin/linker to prevent movement of domain segments? I know that this is not the way to study ligand-protein interaction, however I just want to use it for understanding which topology generation method is better. Thank you!
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