I have pdp files but the format is not supported even it mentions that pdp is the accepted format
Welcome @chadi_ouechtati
Do you mean a pdb file? If yes, this is the datatype the tool is expecting to process. Your dataset in the history should have this datatype assigned for the input select filters to recognize the dataset.
The Upload tool can probably assign this if you load the data with all defaults but you can also adjust this (after confirming the content).
If all of that is correct, make sure the history with the dataset is the active history. You can check on the Activity Bar → Histories view, then load the tool form again after the switch.
If this what you have done and there is still a problem, would you like to share some screenshots to explain more? Please make sure to expand the input dataset to show the metadata.
Let’s start there, thanks! If you solve this, please let us know! 
Example → https://usegalaxy.eu/u/jenj/h/example-align-structures-and-compute-relative-rmsds