I am getting the following error message when I try to extract pdb files from a silent file (output from ligand docking using RosettaScripts).
core.io.silent.SilentFileData: Reading 1 structures from silent.out core.io.silent: parse error: found 0 RT lines for a fold-tree with 2 for decoy tag complex_mat1_0016 caught exception failure to read decoy complex_mat1_0016 from silent-file silent.out
I'm using the following options: "-in:file:silent silent.out -in:file:tags complex_mat1_0001 -extra_res_fa a.params b.params"
When I looked inside the silent file, I do see that the lines that start with "RT ..." is missing for complex_mat1_0016. First of all, I do not know what this means and why some structures (0016 happened to be the first one, but there are more following that are missing the RT lines) are missing these RT lines.
In the end, this file is not what I am looking to extract the pdb of, so if there is a way to bypass validation of every structure in the silent file, that would be helpful, too.
Thank you in advance!
EDIT: I still haven't figured out what the problem is yet, but I wanted to provide some more information for anyone who could try to help me out.
1. I've updated rosetta with the latest weekly update, and I still get the same parse error on these silent files. (Now there is a nice "[WARNING]" in front of parse error with the update)
2. All my silent files were prematurely terminated due to a timeout error on the cluser I am using. But I don't think this is the problem, because I went back to a silent file from before, which had no trouble being processed by extract_pdbs, and now it's throwing the same error where there are some structures with only one RT line and extract_pdbs application doesn't like it.
3. As alluded from the previous point, the extract_pdbs application (from the same old version) used to work just fine last time I used Rosetta, which was about 3 months ago. One of the biggest changes I made between then and now was that I changed the directory of rosetta, but I've rebuilt all the applications numerous times since then.
4. When I manipulated the silent file and got rid of all the lines following the 0016 structure, extract_pdbs application worked just fine and outputted a pdb.
Ultimately, I would like to get down to the root of the problem, as some structures that I would like to extract pdbs of do have only one RT line...
Could someone give me a pointer at least by explaining what the significance of these RT lines is? Thank you!!!