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The problem is my pack.xml specified a resfile.txt location which over-wrote my command-line option. <TASKOPERATIONS> <ReadResfile name="Design_Resfile" filename="resfile.txt"/> </TASKOPERATIONS> If you remove the filename option in the XML file, you are then able to specify the path. <TASKOPERATIONS> <...


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Unfortunately you do in general increase your chance of success by going to the 50k range of models or higher. Projects like Rosetta@home exist because even large research groups can't access as much compute power as they'd like. In this case the long time arises from the combinatorial explosion of possible fragment combinations that need to be explored. ...


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Per Atom You are correct. Rosetta scorefunction does not store any per atom data. The scoring operates at the per residue level. Whereas each atom has its coordinates and properties in full atom mode, in Pyrosetta it is clear that an atom is a just part of a residue and every operation is applied at the residue level. It's a team effort: the functional group ...


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The Rosetta ref2015 is well described in two papers, which I wish I had read much earlier, see this JChIM paper. It's a statistical forcefield, where the terms are weighted to best match the empirical total energy in kcal/mol and the paper does a swell job at explaining what they do. For several Rosetta experiments, you switch between full-atom and centroid (...


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Some force-fields rely solely on theoretical physical principles, while others are tweaked specifically for the goal of accurately depicting certain structures like sheets and helices or movement/diffusion aspects at different theoretical temperatures of a set of well-studied proteins. (Top-Down vs. Bottom-Up) I haven't done MD myself but I am in an MD group ...


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