Connecting a 6500 to a Yaesu VL-1000 amp does not work

I assume you have the PTT cable connected to the TX1 jack on the 6500. Make sure that TX1 is enabled in the radio setup menu TX Tab as described in section 33.6 of the SmartSDR manual.

73,
Craig, KØCF

I had the same setup Quadra and 6500 and it worked fine. You have to make sure the appropriate TX is enabled. Go to Settings, Radio Setup, TX. Depending on which RCA TX line you connected the Quadra to, you will need to enable it.
At the time there was no USB cables for 6xxx so I used DDUtil and a parallel port card on the PC to send band data to the Quadra. Now, you just get the proper USB to parallel cable and set it up. I've since upgraded to the 6700 and using my winter time amp Alpha 87A as it warms up the shack a bit. I have not done this yet but I'm this is the procedure to follow, it should work:

The USB to parallel adapter I used was:
https://www.amazon.com/gp/product/B00HKK4SCO/ref=oh_aui_detailpage_o00_s00?ie=UTF8&psc=1

but Flex also has one you can buy, http://cart.flexradio.com/USB-to-Parallel-adapter-for-the-FLEX-6000-series_p_1001.html

Plug in the cable to one of the USB ports on your 6500, select USB Cables in the SmartSDR Settings menu, you should see the new cable, make these changes:

• Name: Quadra
• Cable Type: BCD
• Source: TX Slice
• Type: HF-BCD
• Polarity: Active High (default)

You will need a male DB-15 connector that would connect to the back of the Quadra to VL-1000’s BAND-DATA 2. You will also need an appropriate length of at least 5 conductor cable to from the Quadra to the back of your 6xxx.

• brown (BIT4) on USB adapter to pin 7 on DB-15 connector
• green (BIT3) on USB adapter to pin 6 on DB-15 connector
• yellow (BIT2) on USB adapter to pin 5 on DB-15 connector
• orange (BIT1) on USB adapter to pin 4 on DB-15 connector
• black (ground) on USB adapter to pin 3 on DB-15 connector