Recently, I took advantage of resfile syntax to refine rosetta docking and backrub results.
But I met three problems, and would be happy to get any comments from others.
First, a nice simulation result pushed me to preserve some Ca ions in the input PDBs, whereas even if I have already supplemented a resfile including 'xx A NC CA', it was still interrupted on the way and shown like that 'aa CA is an unrecongnized aa'. Then I checked PDB file and found that Ca ions were listed in the last lines, so I moved them to related bound amino acids positions in the file and treated them as single atoms. However, nothing seemed to be changed. How could I keep these Ca ions?
Second, if the metal ions were circled in a loop and there was no further information about its specific bound single amino acid, could I define that all those amino acids covering the loop were allowed to obtain Ca, otherwise I must designate only one amino acid?
Third, usually I would have to add a spin label(uncommon organic group) to cystenine in my research, how could I make it go through the reading file checking in backrub application, since such checking always discarded my spin label and inputted it as a cysteine? Do I must write a file similar to those in rosetta_database/chemical/residue_type_sets/fa_standard/patches? If so, how partially distributed charge on each atom was calculated, empirical or what else?
Thank you for all.