How you combine silent files depends on the type of silent file you use.
Ligand docking used a format called “AtomTreeDiff”, which required a specialist program to combine the structures.
I’m guessing that the silent files that you have from FlexPepDock are of the “protein” or “binary” silent file format. These formats are set up for simple concatenation – that is, using the commandline you propose should work. Alternatively, we have programs which will do the combination for you. For example, the combine_silent application:
combine_silent.linuxgccrelease -in:file:silent decoys_1.silent decoys_2.silent decoys_3.silent -out:file:silent decoys.silent
The benefit of this is you can control the output file format (e.g. by adding “-out:file:silent_struct_type binary”) or only extract and combine certain structures, by using the “-in:file:tags” option.
For the simple use cases, though, the “cat” approach works just fine.
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