I am writing here after so much struggle with incorporation of NCAA (Bpy-Ala) using different rosetta scripts like:
Fixbb, rosetta_script with xml file indication point mutation as well as suggested methods in BCL_Tutorial_2022. I am able to add Bpy-Ala at desired position but my problem is different. There are two N-N atoms in bipyridine ring connected via rotatable bond. During the design process, rotamer libraries are selected, or the bond between two aromatic rings rotate such that two N-N atoms move away. These atoms are going to make interactions with metal Ion (Ni or Co).
In order to fix two N-N in the same conformation and to interact with metal Ions, i tried several ways to restrain the aromatic chi angle (ex1aro:level 0 etc) but it does not work.
If I use only mutate function:
<ROSETTASCRIPTS> <MutateResidue name="design" target="99" new_res="BPY" preserve_atom_coords="true" mutate_self="false" /> <ROSETTASCRIPTS>
I can add Bpy-Ala and the N-N atoms are also in the right direction. But by simple addition of bulky NCAA i get lot of side chain clashes with AA. Once i try to remove clashes by adding FastRelax, the N-N atom conformation changes again.
<MOVERS> <MutateResidue name="mutate" target="$i" new_res="BPY" preserve_atom_coords="true" mutate_self="false" /> <FastRelax name="relax" scorefxn="REF2015" repeats="10"> </FastRelax> </MOVERS>
I tried to use the rotamer flags as following to fix rotamer conformations as well:
-use_input_sc -ex1 -ex2 -packing:ex1aro -packing:ex1aro:level 0 -packing:ex2aro 0 -packing:ex2aro:level 0
but it also does not help.
Then I thought of following the original paper from 2013: 10.1021/ja403503m,:
""The theozymes were then split into two parts: the Bpy-Ala residue bound to a virtual metal atom, and a dopamine molecule, also bound to a virtual metal ion. The split theozymes were converted to Rosetta parameters with the script:
I therefore tried to make param file for Bpy-Ala + Metal using
but it failed to recognize the metal ion. I dont know the trick how to run molfile_to_params.py to generate theozyme parameters.
I would be thankful to any suggestion or help to solve/fix this issue.
I think the unrecognized problem should be related to your metal ions. Do your metal ions bring charges? If so you may check <path-to-Rosetta>/main/database/chemical/atom_type_sets/fa_standard(or the mode you want to use)/atom_properties.txt and other files as well. You should check if your wanted metal ions are in the text, else you need to add their properties mannually. Rosetta now only support part of metal ions, so if you want to use new metal ions, you need to check if Rosetta can recognize it first.
I hope this can help you. Best wishes.