How can I select a ragdoll entirely as a rigidbody in animation

I am trying to make a character controller with a ragdoll. So far I have made the character move in ragdoll state with the arrows keys. The problem is that I want to add the animations, and when I do, the ragdoll becomes kinda static.

The problem I have is I want to add the movement animations. And while the character moves, I want it to have a rigidbody that acts like a general collider. I dont want to use a character controller collider. So far it works when there is no animation, like idle or run.

The main problem arises when I activate an animation. Then all the ragdoll colliders kinda like disspear, and they are not detected, when there is an animation. Why this happens???

This is my code:

 public static TP_Controller Instance;
 public static Rigidbody rb;
 public static Transform ragdoll;
 GameObject Piso = GameObject.Find("Piso");
 public LayerMask mask;


 RaycastHit hit;

 public bool isgrounded;

 // SIMPLE RAGDOLL

 Animator animator;

 public static Rigidbody[] rigidbodies;
 public static Transform[] rigidTransforms;

 Vector3[] lastRigidPositions = new Vector3[1];
 Vector3[] rigidVelocities = new Vector3[1];
 Vector3[] rigidAngularVelocities = new Vector3[1];
 Quaternion[] lastRigidRotations = new Quaternion[1];

 [Range(0f, 1f)]
 public float veclocityLerp = .2f; // If zero, then no momentum will be transferred to the ragdoll
 [Range(0f, 1f)]
 public float keepAngularMomentum = .4f; // If zero, then no angular momentum will be transferred to the ragdoll
 [Range(0f, 240f)]
 public float angularDrag = 30f; // Rigidbodies angular drag. Unitys parameter
 [Range(0f, 4f)]
 public float drag = .5f; // Rigidbodies drag. Unitys parameter
 float maxAngularVelocity = 100f; // Rigidbodies maxAngularVelocity. Unitys parameter

 public bool useGravity = false; // Ragdoll is affected by Unitys gravity
 public bool ragdolled = false; // Instantiate ragdoll with same pose and momentum as master

 

 public void Awake () // Debe quedarse en awake
 {

     

     ragdoll = transform.FindChild("Armature") as Transform;
     rb = ragdoll.GetComponentInChildren(typeof(Rigidbody)) as Rigidbody;

     Instance = this;

     animator = GetComponent<Animator>();


     rigidbodies = GetComponentsInChildren<Rigidbody>();

     int i = rigidbodies.Length;
     System.Array.Resize(ref rigidTransforms, i);
     System.Array.Resize(ref lastRigidPositions, i);
     System.Array.Resize(ref rigidVelocities, i);
     System.Array.Resize(ref lastRigidRotations, i);
     System.Array.Resize(ref rigidAngularVelocities, i);

     i = 0;
     foreach (Rigidbody rigidbody in rigidbodies)
     {
         rigidTransforms[i] = rigidbody.transform;
         i++;
     }

     i = 0;

     foreach (Transform rigidTransform in rigidTransforms) // Set some of the Unity parameters
     {
         lastRigidPositions[i] = rigidTransform.position;
         lastRigidRotations[i] = rigidTransform.rotation;

         rigidTransform.rigidbody.useGravity = useGravity;
         rigidTransform.rigidbody.angularDrag = angularDrag;
         rigidTransform.rigidbody.drag = drag;
         rigidTransform.rigidbody.maxAngularVelocity = maxAngularVelocity;
         rigidTransform.rigidbody.isKinematic = false;
         i++;

         }
     if (i == 0)
         Debug.LogWarning("There are no rigid body components on the ragdoll " + this.name);
         

 }
 

 void Update () 
 {
     if (Camera.mainCamera == null)
         return;

     GetLocomotionInput();

     TP_Motor.Instance.UpdateMotor();


     IsGrounded();



 }

 void IsGrounded()
 {

     RaycastHit hitInfo;
     if (Physics.Raycast(rb.transform.position + Vector3.down * 3f, Vector3.up * 5f, out hitInfo, Mathf.Infinity, mask))
     {


         if (hitInfo.distance > 0.1f) // Change .1f to what you need
             Debug.DrawRay(rb.transform.position + Vector3.down * 3f, Vector3.up * 5f, Color.blue);
         
         isgrounded = true;

      }
         

         if (hitInfo.distance  < 0.5f){
             Debug.DrawRay(rb.transform.position + Vector3.down * 3f, Vector3.up * 5f, Color.red);

         isgrounded = false;
     } 
  } 

 void GetLocomotionInput()
 {

     var deadZone = 0.1;

     TP_Motor.Instance.VerticalVelocity = TP_Motor.Instance.MoveVector.y;
     TP_Motor.Instance.MoveVector = Vector3.zero;

     if (TP_Controller.Instance.isgrounded != false)
     {
     if (Input.GetAxis("Vertical") > deadZone || Input.GetAxis("Vertical") < -deadZone)
         TP_Motor.Instance.MoveVector += new Vector3(0, 0, Input.GetAxis("Vertical"));

     if (Input.GetAxis("Horizontal") > deadZone || Input.GetAxis("Horizontal") < -deadZone)
         TP_Motor.Instance.MoveVector += new Vector3(Input.GetAxis("Horizontal"), 0, 0);
     }
 }

}