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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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Implement Gaussian surface definition (with Zap help) #89

Closed sobolevnrm closed 4 years ago

lizutah commented 10 years ago

more info, @sobolevnrm ? found: http://www.eyesopen.com/zap-tk http://onlinelibrary.wiley.com/doi/10.1002/prot.23079/full

sobolevnrm commented 10 years ago

The algorithm is described at

Grant:1995

A Gaussian Description of Molecular Shape

J. Grant and B. Pickup

J. Phys. Chem. 99 3503--3510 (1995)

http://dx.doi.org/10.1021/j100011a016

Grant:2001

A smooth permittivity function for Poisson--Boltzmann solvation methods

A. Grant and B. Pickup and A. Nicholls

J. Comput. Chem. 22 608--640 (2001)

http://dx.doi.org/10.1002/jcc.1032

This work introduces a continuous smooth permittivity function into Poisson--Boltzmann techniques for continuum approaches to modeling the solvation of small molecules and proteins. The permittivity function is derived using a Gaussian method to describe volume exclusion. The new method allows a rigorous determination of solvent forces within a grid-based technology. The generality of approach is demonstrated by considering a range of applications for small molecules and macromolecules. We also present a very complete statistical analysis of grid errors, and show that the accuracy of our Gaussian-based method is improved over standard techniques. The method has been implemented in a new code called ZAP, which is freely available to academic institutions.1 ©2001 John Wiley & Sons, Inc. J Comput Chem 22: 608--640, 2001

On Fri, Oct 17, 2014 at 12:06 PM, Liz notifications@github.com wrote:

more info, @sobolevnrm https://github.com/sobolevnrm ? found: http://www.eyesopen.com/zap-tk http://onlinelibrary.wiley.com/doi/10.1002/prot.23079/full

— Reply to this email directly or view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/89#issuecomment-59560394 .

keith923 commented 10 years ago

I read that paper!! I'm so easily excitable...

What's "Zap help"?

sobolevnrm commented 10 years ago

Sorry; can you provide more context on the question about "zap help"?

On Tue, Oct 21, 2014 at 3:55 PM, Keith T. Star notifications@github.com wrote:

I read that paper!! I'm so easily excitable...

What's "Zap help"?

— Reply to this email directly or view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/89#issuecomment-59988099 .

lizutah commented 10 years ago

I think @sobolevnrm was implying that we look into using the zap code base for implementing gaussian surface definition?

keith923 commented 10 years ago

I was just replying to this as well. I was referring to the title @sobolevnrm!