Dear Modellers,
I have three points to discuss.
1) As I changed the optimization protocol, I woul dlike to check if my set up has been done. Where could I check it?
2) I am building a multimeric protein. The DOPE and GA341 scores are developed for single chain models. How can I asses the quality of my models? The sole molpdf is sufficient?
3) I found thie messagge in the log file:
Treating residue type GSH as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file.
I have understood that the input PDB file is the .ini, which is written during the calculation. Thus, how can I "remove the corresponding 'MODELLER BLK RESIDUE" to treat the residue flexible? Have I to define it as my own residue?
Thank you in advance
All the best
Simone