Dear all,

After installing cryo_fit in phenix and gromacs_cryofit on my Macbook Pro M1, I now try to test the code using the example data GTPase.

The job encounters immediately a problem but the GUI suggests that the job is still running.

The log suggest that the first step did not run successfully (below). I presume setting the topology of the protein but I don’t know.

Another question is how is it possible to set other parameters for cryo_fit (like ff…) in the GUI or should I run it in command line ?

Thank you for your help and suggestions.

Philippe.

User's computer's operating system: Darwin

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#################### Step 1: Make gro and topology file by regular gromacs ####################

###############################################################################################

Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1/steps/1_make_gro

command: python 1_before_pdb2gmx_prepare_pdb.py GTPase_activation_center_tutorial.pdb 0 0 0 True

Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1

This pdb file, /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/GTPase_activation_center_tutorial.pdb , has 6489 atoms

Approximately, for this number of atoms, one 3.1 GHz Intel Core i7 took 7 seconds to make a gro file.

command: python 2_runme_make_gro.py /Applications/phenix-1.20.1-4487/modules/cryo_fit/ amber03 True True /usr/local/cryo_fit/cryo_fit/bin//

Step 1 didn't run successfully

User's command was

phenix.cryo_fit /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/.phenix/project_data/run_1.eff

phenix.cryo_fit alone without any arguments introduces full options.

If a user sees a message like

"Fatal error:

Atom xx in residue xx xxx was not found in rtp entry xx with xx atoms

while sorting atoms."

or

"Fatal error:

Residue xxx not found in residue topology database"

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 fixed.

If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add appropriate parameters.

If you added parameters, please email me ([email protected]), I want to recognize your contribution publicly.

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 user's input 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 later.

Email [email protected] or [email protected] for any feature request/help.