ORF2 and Isoprenoid Biosynthesis

Isoprenoids or terpenoids are a large class of naturally occurring organic compounds with tremendous chemical and structural diversity. They are organic materials produced in the HMG-CoA (3-hydroxy-3-methyl-glutaryl-CoA) reductase pathway 

1ZDY 16.70 1.44 N- (tris (hydroxy methyl)methyl)-3 -aminopropanesulfonic acid 

Unlike the native integration of DIVCON with the sander module in AMBER, the integration of CNS was done at the file system level. For every step of hybrid minimization, CNS, after receiving atomic coordinates from sander, calculates and outputs the forces as the gradient of Ex-ray in Eq. (13-11), which is then read by sander. Sander combines the forces from Ex-ray and Eqm/mm potential and updates the coordinates accordingly. This process proceeds until the R and free R factors converge, which usually takes a few hundreds of steps. 

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