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In my MD running, by using the amber99SB force field, but there is a non-standard residue, phosphorylated Aspartate, no parameters for this residue. How do I generate parameters for this residue?
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In a homodimer protein, several residues' side chains were missed in A chain or B chain. How can I use the same residue of the other chain to build/complete these missed side chains? How can I...
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