I am trying to use "loop_length_changing". The demonstrating file is straightforward.
Can I ask
1) How to specify the loop file?
The demonstrating loop file uses "LOOP 18 28 21 0 0" to loop ALA 21-25. As I understand, three residues before (i.e. 18-20) and after (i.e. 26-28) are also included in the looping region. The cutpoint 21 should refer to the actual loop starting point. Can I ask if I understand correctly? I am still quite confused about the meaning of "cutpoint" (the 3rd number).
In my case, I want to loop a region of 136-139. So should I use "LOOP 133 142 136 0 0"?
2) Should I include the option "-nstruct"? If so, how many should be sufficient, like 1000 ?
3) Can I specify the chain identity? I have heavy chain (HC) and light chain (LC), and now I have to do it separately.
Thank you very much.