Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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Chapter 7: <strong>Prime</strong>–Refinement<br />
<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong><br />
Figure 7.2. The Energy Analysis task in the Refinement panel.<br />
7.4 <strong>Prime</strong> Energy Analysis<br />
To perform a single-point molecular mechanics energy calculation, choose Energy Analysis<br />
from the Task option menu. The calculation uses the OPLS_2005 all-atom force field for<br />
protein residues as well as for ligands and cofactors. If desired, set up an implicit membrane<br />
model. Click Start, make job settings in the Start dialog box, then click Start to run the job.<br />
The output includes a breakdown of the energy into covalent, Coulombic, van der Waals and<br />
solvation energy contributions. Each of these is added as a Maestro property to the output<br />
structure file, named <strong>Prime</strong> Covalent, <strong>Prime</strong> Coulomb, <strong>Prime</strong> vdW, and <strong>Prime</strong> Solvation. The<br />
output also includes a breakdown of the energy on a per-residue basis.<br />
7.5 Refining Loops<br />
<strong>Prime</strong>–Refinement is capable of refining loop structures of various lengths, and provides algorithms<br />
for different loop lengths. In addition, loops whose structure affects other loops can be<br />
cooperatively refined in pairs.<br />
To refine one or more loops serially:<br />
1. Choose Refine Loops from the Task menu.
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