# core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP

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core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP
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core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_DHD
core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP

DHD is the substrate and NAP is the cofactor. Does the above log mean that DHD and NAP are rotated? After refine, the substrate becomes distorted and the coenzyme position changes. How can the substrate and coenzyme not be rotated? I added movemap to the flag file, but "the following options have been set, but have not yet been used:
-in:file:movemap movemapfile"

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Wed, 2022-09-14 06:06
to-qinbin@163.com

The "simple Rotamer generation logic" here is actually indicating that there isn't any active sampling of the heavy atom coordinates. That is, since no other rotamer sampling behavior was specified (e.g. in the params file), Rosetta is keeping the specified (heavy atom) conformation. There is some conformational sampling of things like hydrogen atom placement and explicitly specified bond sampling, which is why it's "simple" rather than "no".

My guess is that the distortion of the ligands aren't coming from any refinement, but rather from the read-in. You can confirm that by passing the structures through score_jd2 -- set your input and params file flags as you would for refinement, and then specify -out:pdb. This will cause Rosetta to read in the structure and write it back out again without any deliberate movement of the coordinates. If you see coordinate changes there, that indicates that it's the process of reading in the structure and the associated automatic normalization which is causing issues, rather than any sampling.

One possibililty is atom naming issues. Rosetta uses the atom names to figure out how to map the coordinates in the input PDB to the atom identities specified in the params file. If these don't match, then you can get structures which look distorted or scrambled. The best way of fixing this it to use a method which matches the atom names in the input with the atom names specified by the params file. Another approach would be to use the -remap_pdb_atom_names_for option (e.g. -remap_pdb_atom_names_for DHD NAP) to tell Rosetta to use some connectivity heuristics to try renaming the atoms. This can be hit-or-miss, so the recommendation would be to use it with score_jd2 and -out:pdb, check to make sure the structure is decent and use that as futrther Rosetta input (without the -remap_pdb_atom_names_for option). The pass through score_jd2 with -remap_pdb_atom_names_for  will renormalize the atom names to the ones Rosetta expects based on the params file.

Wed, 2022-09-14 09:14
rmoretti