Thanks,professor. But my crd file which produced together with this output file has many errors read by VMD as following.
error> Base molecule :Excessive bonding errors encountered,perhaps atom coodinates are in the wrong units?
error> Base molecule :Silencing bonding error messeges.
<warning> Unusual bond between residues: 3 <protein> and 11251 <water>
I am sure that my initial model before putting into the water box is minimized without error.
I do not know what caused this.