My Toyota Tundra 2000 had a flat battery, due to my driving it so little. My son rigged up a trickle-charger as a long term solution & hooked it to the flat battery. He unlocked the truck doors with the remote to access the cab. Then after hooking up charger he used a key in the driver side door when lubing the lock. That seemed to trigger the truck alarm--started clicking under the hood. Now the charger is working but I think the alarm drains the little charge and I am back to zero. Locking the doors manually has not turned off the alarm. Trickle charger has been running for two days. Key fob does not work doors now.

SOURCE: drivers door power lock wont work.

Either the wring going to that motor or the motor itself is bad.

SOURCE: Left side door locks not working at all. Only manually or with key.

When I first read this I thought Solenoid/Lock motor.
But as it's two doors on the one side I would look for a problem with wiring /connections at vulnerable points. Where the wiring goes from the front door to the body is a good place to start.

SOURCE: when we use our key fob to lock the doors, i know

You should be able to just unlock the door with the key, and even if the alarm is still going of try to start it the key should override the alarm.

SOURCE: 1999 Toyota Avalon, key fob locks doors, but will

hello the identical thing is happening to me did you find out what was wrong? regards Ellen

SOURCE: I've been using my key

Open the driver's door and climb in. Insert the key into the ignition and quickly pull it out. Do this twice within five seconds.

2 Close the driver's door and open it again. Reinsert the key into the ignition and pull it out. You must do this within 40 seconds.
3 Shut then open the driver's door twice again. Insert the key into the ignition. Close the door. Turn the key to the "On" position but do not crank the engine, Turn the key to the "Off" position and remove it. This must all be done within 40 seconds. If you have done everything properly, the door locks will cycle from unlocked to locked and back again within four seconds. If they do not, repeat this process.
4 Hold down the "Lock" and "Unlock" keys on the remote for one and a half seconds.
5 Press the "Lock" button on the remote for two seconds. The door locks will cycle again indicating successful programming.