I'm doing docking peptides to kinase structure by using flexpepdock. In the meanwhile I need ATP in the kinase structure, therefore I generated a param file for ATP. But after the prepack mode, the ATP has been removed from the pocket to the somewhere in the structure. Here is my question:
1) how should I fix the ATP in the pocket without any movement? Movemap or constrain file?
2)I was told to use movemap to fix the ATP. But I don't know how's the rosetta numbering of the HETATM.
for example, chain A is from 2-280, chain B is from 2-9, ATP(HETATM) is 381 in the chainA. In this case, which number is the ATP rosetta numbering?