# pmut_scan_parallel

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pmut_scan_parallel
#1

I am new to Rosetta Software, and currently trying to run pmut_scan_parallel https://www.rosettacommons.org/docs/latest/application_documentation/design/pmut-scan-parallel#mutant-list-file-format

I can run this program and get output like:

protocols.pmut_scan.PointMutScanDriver: mutation   mutation_PDB_numbering   average_ddG   average_total_energy
protocols.pmut_scan.PointMutScanDriver: H-Q1A,H-Q3E   H-Q1A,H-Q3E      -1.702      800.50
protocols.pmut_scan.PointMutScanDriver: H-Q1A,H-Q3H   H-Q1A,H-Q3H      -2.686      799.51

Howver, I dont want to scan all residues, but only in specific region. There is option given in above link:

-mutants_list <file>                             Only make the mutants specified in the text file. Useful for combining mutants found during a scan into higher-order mutants. Not used by default.

But I dont know how to assign specific residue which should be mutated with all 19 residues. First of all it gives me error if I use following file:

# a single mutant
H W 33 A

I get no output, only something like this:

protocols.pmut_scan.PointMutScanDriver: go(): master node
protocols.pmut_scan.PointMutScanDriver: mutation   mutation_PDB_numbering   average_ddG   average_total_energy
protocols.pmut_scan.PointMutScanDriver: main(): whole protocol took 103.07 seconds
protocols.pmut_scan.PointMutScanDriver: go(): DONE with pmut scan.

also, as shown in mutant list file, I do not want to mutate W33 to ALA but to all 19 residues. Is there any way to do this and get 19 mutations for single amino acid and 400 mutations for double mutants?

with kind regards

Mustafa

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Wed, 2018-10-17 05:41
G Mustafa