The option out-pdb is setted to true by default. For any of the mutations you carried out you will get a PDB for the WT reference and another one for the mutant both numerated from 0 to .....X.
PDB INPUT | WT | MUTANT |
| 1aay.pdb | WT_1aay_0.pdb, WT_1aay_1.pdb... | 1aay_0.pdb, 1aay_1.pdb... |
1aay.pdb (numberOfRuns=2) | WT_1aay_0_0.pdb,WT_1aay_0_1.pdb, WT_1aay_1_0.pdb,WT_1aay_1_1.pdb... | WT_1aay_0_0.pdb,WT_1aay_0_1.pdb, WT_1aay_1_0.pdb,WT_1aay_1_1.pdb... |