I am using FlexPepDock to dock a peptide to a target. The target has a loop which has missing electron density for 6 residues, and I want to compare how filling in this loop will affect FlexPepDock poses - the loop is too close to the docking position of the peptide for me to be comfortable not dealing with this situation.
It is not clear to me how to proceed. I have the following questions:
1. The overall loop is ~21 amino acids. Presumably, I can just remodel the missing 6 residues. Is this assumption correct?
2. What is the best way to have an initial PDB to feed into the loop remodelling/building protocol. I have tried writing dummy xyz (0.0 0.0 0.0) co-ordinates in a text editor for the six residues, renumbering this modified PDB in pymol (both atom ID and residue number) and then passing this through KIC remodel and refine, but this fails to build the loop with the following error;
protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: [WARNING] Failed to build loop with kinematic Mover during initial kinematic perturbation after 100 trials: LOOP 145 149 148 0 1
protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: Unable to build this loop - a critical error occured. Moving on ..
3. I am now going to try the "-build_initial" flag using the non-KIC method, but if anyone has a better solution, please do let me know.