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I ran this command:

run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./folder 10 500 

From my previous discussion, I understand that I should run with default "run_dmpfold.sh" parameters i.e. 3 50; however, since I have already run the 10 500 I have some questions.

I see that after generating "sequence_1.pdb to sequence_500.pdb" files, these files are no more in the folder and, now I see "ensemble_1.pdb". Will there be more ensemble files like "ensemble_500.pdb" and "sequence_n.pdb" files? I mean when can I expect "final_1.pdb' file? Also, I see files like "CLUSTERS_001.pdb".

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The sequence_n.pdb files are temporary and are combined into an ensemble.i.pdb file after each iteration i. That file has many structures in. After the run is complete there will be a final_1.pdb file. Don't worry about the cluster files. If you are interested in what they do, consult the run_dmpfold.sh script and see what it is doing line by line.

As I have said multiple times elsewhere, you should run the script with default parameters and let it run to completion. Then use the final_1.pdb and any other final_*.pdb files as the output. If you want more structures, use the ensemble.i.pdb files.

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