The discovery of potential drug to arrest the replication of HIV-1 even in these modern days is a growing task. Drugs in market are targets the enzymes reverse transcriptase, integrase and protease. The encapsulation gene of HIV genome that is GAG is found to be more conserve. So the functional and structural conservation of HIV-1 Gag implies structure based drug design. Now HIV-1 replication can be successfully blocked by targeting gag polyprotein, a new promising avenue for the drug class. Gag’s role is helping in forming the encapsulation of the virus if that is disturbed the whole Virus is vulnerable. The challenge is to determine the structure of Gag poly-protein as its structure is still unknown. The crystal structure is unavailable in the structural databases like PDB. The sequence of gag polyprotein of HIV1 group M subtype B (isolate JH32) (HIV-1) was downloaded to determine its structure. As there is no template close to the target a method called refinement through multi threading was used. The percentage of favored regions by Ramchandran diagram is 89.6%, allowed region is 5.0% and amino acids in outlier region is 5.4%.