Sign the key. Format is as follows, your key is the signer:
pgp --sign-key 0x12345EC1 --signer 0xXXXXXXXX --sig-type local -p YourPassphrase
--sig-type is the signature type: local, exportable, meta-introducer, or trusted
introducer. Usually I recommend local unless you plan on distributing this key later to others, or you want to automatically verify keys that have been signed by the imported key in the future.
Then set the trust:
pgp --set-trust 0x12345EC1 --trust complete
Only use the complete trust if you are absolutely certain that it belongs to the appropriate person/company. In most cases, it is easy to verify (e.g. Bob emailed you his public key, so you know that the email associated with the key should be correct). If nothing else, you can call the other party and confirm the KeyID with them.
Now it should be a simple matter of encrypting:
pgp -e YourFileName -r 0x12345EC1 --output NewFileName.pgp -v
You can use User ID's instead of key ID's in most places if desired. The -v at the end just provides a verbose output of the process to be displayed in the command prompt. If you would like this to be output in a file for future reference, you can also add this to the end:
--output-file OutputFileName.txt