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Hello, everyone, I encountered some problems when I was doing Step 19: Actual motif grafting of RIFdocking.
First, I need to turn my scaffolding into a silent files. The command is as follows:

cat scaffolds.list | silentfrompdbsparallel > scaffolds.silent

After the command is run, I got the following error:

Hello,

I have been running this command other pdbs:

python2.7 /mnt/c/Users/No\ LOL/Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/tools/protein_tools/scripts/pdb_renumber.py \--norestart HER2_C_G3_A_full.pdb HER2_C_G3_A_full.pdb

and it has worked. Yet when I run it for my current pdb, it produces this error:

Hello, i am trying to relax an enzyme with a co-factor (nadp) but whenever I do, the resulting structure looks wrong.

I use the NADP structure from pubchem as a starting point, then molfile2params structure  and copy paste the returned LG_0001.pdb to my protein. 

i then run the following code: