The B server (http://www.scripps.edu/ ~ nwhite/B/indexFrames.htmp offers an online biomolecular modeling program that builds biomolecular models, measures their geometry, and implements an AMBER force field in the geometry optimization as well as in molecular dynamics. The Biomer authentication certificate (see http:// www.scripps.edu/ ~ nwhite/B/Security/) is required to enable opening/saving files
(though it is not needed to run the B program).
• Click the Start B button to open the B window.
• Hit the Grant button to the Biomer certificate to open the file browser box.
• Select Polynucleotide/Polypeptide/Polysaccharide from the Build menu to open a dialog box.
• For polysaccharide, choose connectivity (O1 -C[1 -6]), anomer (alpha or beta), isomer (l or d), and conformation (define phi and psi angle with omega = 180). Add sugars (alsohexoses or aldopentoses) to build polysacchar-ide chain.
• For polynucleotide, choose various options such as either DNA or RNA, Form (a, b, c, d, e, t, or z forms), Build (5' to 3' or 3' to 5'), single strand/double strand, and conformation of pentofuranose ring. Add bases (pairs) in the specified direction to build polynucleotide chain.
• For polypeptide, the B program provides options for building various protein conformations including 3 -10 helix, alpha helix, alpha helix (L-H), beta sheet (anti-prl), beta sheet (parallel), various beta turns, extended, gamma turns, omega helix, pi helix, polyglycine, and polyproline. Choose the desired conformation and isomer (l or d) and then add amino acids from N-terminus to construct polypeptide chain.
• Cap the termini if desired for polypeptide or polysaccharide. Click Done button to view the molecule on the display window (Figure 15.8).
The Tools menu provides utilities to calculate net mass, net charge, energy and to invert chirality. For energy minimization,
• Select the Molecular mechanics menu and choose Steepest descent as the initial Minimizer that can be changed to Conjugated gradient later.
• Click Minimize to start energy minimization. The gradient and energy are displayed on the lower left corner of the display window.
For dynamic simulation,
• Select the Molecular dynamics menu to open the dialog box. Specify Time, Temperature, and Step size for Heating cycle, Equilibrium period, and Cooling cycle.
• Click Start trajectory to initiate simulation. The lower left corner shows the progress of the simulation.
• Click the Grant button to the certificate to save the molecule.pdb.
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