Hello Joseph,
Sorry for late reply, your email was not in my inbox.
I just changed my setting so that email to [email protected] will come to my inbox directly.
Thank you for sharing your input file. I just ran your input pdb file, it appears that "SO4, "CD" are not in amber03 forcefield.
I just added my comments like this
Solution if these residue/atoms are important: Fix wrong names of atoms/residues. Running real_space_refine via phenix GUI will show which atoms need to be removed/fixed
If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add parameters.
It is rather a sad fact that most MD simulation force fields do not support all kinds of rare residue/atoms.
cryo_fit2 is under development to address this issue using phenix.eLBOW
Solution if these residue/atoms are not important:
Remove these \"wrong\" atoms/residues from user's input pdb file. Run cryo_fit again
Solution if your user's pdb file is big:
Probably cryo_fit will change conformation just minimally, I would extract out these \"wrong\" atoms/residues from user's input pdb file, then add these extracted lines to cryo_fitted file
If you do
git pull
at your <phenix>/modules/cryo_fit
and run again, you will see results at least to the final stage (that I can't run because of lack of map).
best regards,
Doonam
________________________________
From: Finney, Joseph (NIH/NCI) [C]