Plop (Protein Local Optimization Program) Protein Loop Prediction

Question

[Reyhaneh]

Hi

Has anybody used PLOP (Protein Local Optimization Program) to perform loop prediction. I want to predict the loop which is located between resi 42-46 on chain A of input 2IGD.pdb. My control command looks like this:

datadirectory  /PLOPDirectory/data
file logfile modeled_plop_job.log 
load pdb 2IGD.pdb 
   loop predict A:42 A:46 &     
   ideal yes &     
   nconf_min 30 &     
   pdbfile modeled-output.pdb &

This works if I take the complete pdb file 2IGD.pdb which already contains the loop region 42 to 46. In this case PLOP tries to optimize it. But in reality loop prediction means that the loop area should be missing from the input file. When I remove the coordinates of resi 42 to 46 from the input pdb file PLOP does not work any more. Do you know how to use PLOP when the input coordinates of the loop is missing? how can I input the loop sequence?

Thank you