Abstract: Human immunodeficiency virus is a lentivirus (slowly replicating virus) that causes Acquired immuno deficiency syndrome (AIDS). HIV attached to the human CD4 receptor and leads to the infection. Protein modelling is type of structure prediction from its sequence with an accuracy that is comparable from different softwares .Computational protein modelling is a method designed for the most probable 3D structure from a sequence given its alignments with related structure .In this topic we discuss about the 3D structure of HIV1and HIV2 protein from different softwares and their variations in core value, hydrophobicity, residues and intermolecular forces.