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Hi,

I am doing side-chain packing on a fixed backbone over a discrete set of configurations. Given a set of (non-rotamer) side-chain configurations I'm using Rosetta to calculate one-body and two-body energies using the standard scoring function. I observe to things that seem strange in the two-body energies:

1) For a pair of residues sometimes the two-body energies are almost all zero except for a couple configurations. This sort of makes sense if the residues are far enough apart, but does it make sense that they are *exactly* zero?

Dear friends,
I am trying to use "loop_length_changing". The demonstrating file is straightforward.

rosettademos\public\AnchoredDesign\loop_length_changing

Can I ask
1) How to specify the loop file?

Dear friends,
I am trying to use FloppyTail to determine a C-terminus tail structure of 6 consecutive His residues. However, several residues before the tail also experience conformation change though the majority is remained the same. Can I ask is there a way to only optimise the tail structure?

Dear friends,
I am trying to use "clustering.py" but I was told "OSError: [Errno 2] No such file or directory". Can I ask how to solve this?

I am sorry but it seems I have been asking technical questions all the time. Please tell me if there is something I can read to prepare my knowledge to debug. For example, how can I actually debug this python problem based on the error message?

Thank you very much.

Yours sincerely
Cheng

The following is the command line and prompt.