Hello,

I would like to run MD on a protein with a porphyrin-Fe cofactor. The YASARA-automatized semi-empirical treatment of the cofactor is not working properly when launching MD with the AMBER14 force field, many distortions occur.

With a colleague, we optimized the structure of the cofactor (embedded inside the protein) with Gaussian. Our intention is to assign ab initio-calculated atom charges and other parameters before running the MD in YASARA. However, I don't know how to proceed "to pass" the information to Yasara. I suppose I must "insert" atom types, charges, bond lengths and strengths, torsions, etc, etc in one of the AmberXX.fof files in the fof/ folder (and the run yasara -upd). However, it might be really long to do and worse, I might forget things to include.

Is there any "manner" to do that properly, or it has to be done manually? Could it suffice to transfer the ligand parameter files to the fof folder, separated from the main AMBER14.fof? How to ensure that the cofactor will not be retreated with the AUTOSMILES method by YASARA?

In case it could help, I attach a type of parameters file we obtained with Gaussian. But other formats might be produced if necessary.

Thank you very much in advance for any help,