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URL:
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http://www.charmm-gui.org/?doc=input/pbeqsolver
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What you can do:
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Calculates and visualizes the electrostatic potential of your molecule by solving the Poisson-Boltzmann (PB) equation.
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Highlights:
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- PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue.
- All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane).
- PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users.
- Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org).
- To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 A before and 1 A after focusing).
- PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary.
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Keywords:
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- electrostatic potential
- Poisson-Boltzmann equation
- PB equation
- solvation free energy
- electrostatic interaction energy
- PBEQ
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Literature and Tutorials:
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PubMed Link: PBEQ-Solver for online visualization of electrostatic potential of biomolecules
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