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Prime User Manual - ISP

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<strong>Prime</strong> <strong>User</strong> <strong>Manual</strong><br />

Chapter 10: <strong>Prime</strong> MM-GBSA<br />

Chapter 10<br />

The <strong>Prime</strong> MM-GBSA panel can be used to calculate ligand binding energies and ligand strain<br />

energies for a set of ligands and a single receptor, using the MM-GBSA technology available<br />

with <strong>Prime</strong>.<br />

The ligands and the receptor must be properly prepared beforehand, for example, by using<br />

LigPrep and the Protein Preparation Wizard. The ligands must be pre-positioned with respect<br />

to the receptor, and the receptor must be prepared as for a <strong>Prime</strong> refinement calculation.<br />

To open the <strong>Prime</strong> MM-GBSA panel, choose MM-GBSA from the <strong>Prime</strong> submenu of the Applications<br />

menu.<br />

After preparing your structures, you can set up the calculation as follows:<br />

1. Specify the source of the structures.<br />

You can take structures from a Pose Viewer file (Glide output), or from separated ligand<br />

and protein structures. If you choose the latter option, you must ensure that the ligands<br />

and the protein are properly prepared and aligned.<br />

2. (optional) Choose calculation settings.<br />

If you want to evaluate ligand strain energies as well as ligand binding energies, select<br />

Calculate ligand strain energies. With this option, an extra calculation on the ligand is<br />

performed at its geometry in the complex, and this result is combined with the free ligand<br />

calculation to calculate the strain energy.<br />

If you want to use ligand partial charges evaluated by some other program, such as QSite,<br />

select Use ligand input partial charges. The input partial charges on the ligand will then<br />

be used instead of those assigned using the default force field.<br />

If you want to use the <strong>Prime</strong> implicit membrane model, select Use implicit membrane.<br />

The receptor you choose must have been already set up with the membrane, as described<br />

in Section 7.3 on page 56.<br />

3. (optional) Select a region within a certain distance of the ligand for which the protein<br />

structure will be relaxed in the calculation.<br />

The atoms in all residues within the specified distance of the first ligand processed are<br />

included in the flexible region. By default, all protein atoms are frozen, and only the<br />

ligand structure is relaxed. The larger the flexible region, the longer the calculation takes.<br />

<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong> 81

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