I have the structure of a protein and the cryoEM density map used to generate the structure. I want to use the density map to refine the structure through MD using the GROMACS 2020 density-guided simulation tool. My doubts:
how to treat the pbc with density guided MD and how the size of the boxes should be? How to visualize the size of the density map box?
fitting the protein structure to the density map: any suggestion on how to do it? So far I tried with Chimera without obtaining good results.
I have similar questions/doubts regarding this topic. I am trying to apply the following tutorial https://github.com/moozzz/simulation-protocols/tree/master/cdmd-aldolase-refinement to a different structure. As suggested in the tutorial, I ran gmx editconf -f gmx_structure.pdb -o gmx_structure_box.pdb -bt triclinic -d 1.0 -center x_c y_c z_c (with x_c etc. substituted by center of mass coordinates) to make the box larger and not shift the molecule in respect to the density map. When I checked the files after solvation, the solvent molecules were added around symmetry-related coordinates (but still following pbc I guess). After minimization/equilibration also the protein coordinates were shifted to the symmetry mate in the .gro file which serves as input for the density-guided MD.
Can this shift be a problem for density alignment or is the density also treated in a periodic manner?
Is there a way to avoid this coordinate shift to a symmetry mate in the first place?