Delphi Webserver

Dear Users: Please do not submit large PDB files that require protonation with DelPhiPKa. This causes significant computation and affects the work of other users. Instead, download the stand-alone version of DelPhiPKa and create a PQR file. Thank you for understanding.

Remember, DelPhi webserver uses DelPhiPKa to add protons according to user specified pH. Hence, Delphi jobs may take hours to complete if the PDB file has more than 50 titratable residues, due to DelPhiPKa assessment of protonation states. Please be patient.
If you want the calculations to be fast, provide a PQR file instead.

Delphi Web Server

An online Poisson-Boltzmann solver for calculating electrostatic energies and potential in biological macromolecules

Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group

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DelPhi is a protein electrostatics program, originally developed in Dr. Barry Honig's lab and currently being maintained by Delphi Development team. It utilizes a finite difference method to solve the Poisson-Boltzmann equation for biomolecules and objects within a given system. Its benefits lie in the ability to solve linear or non-linear PB equations while being fast, versatile, and accurate. This webserver provides with an easy, straight-forward, and step-by-step process for using DelPhi for your own interests. Standalone Delphi package is available free of charge for download here.

A quick overview of how everything works:

A biomolecule coordinate file is needed (ie, PDB file format). This PDB file could sequentially be fixed for missing atoms/residues and protonated or the user can upload an already fixed and protonated file.
DelPhi uses charge and size files to gather information on the necessary atoms for your biomolecule. We provide these files as a default option, with them being produced for charmm, amber, or olpsaa compatibility. However, you are free to upload your own charge or size file, if need be.
A DelPhi paramter file is also needed for a successful submission. We provide a default parameter file . However, again, you are free to upload your own parameter file.
As for the results, you are given options for various energies to be calculated along with various visual display maps. For results to be automatically given, the user must provide name and email address.

DelPhi is running on Clemson University's Palmetto Supercomputer cluster. We would like to thank the Palmetto team for hosting this service. We also would like to acknowledge NIH-Grant# 1R01GM093937for supporting this work.

Finally, If these results appear in published papers, we ask humbly to include a reference to our service as defined here.

Upload Structure File:

Upload structure file, in either PDB or PQR format. If you provide PQR file, you will not be able to select pH.

Choose file

Select force field parameters for protonation (Default: Amber)

Specify pH (Default: 7)

Upload CRG file

Choose file

Upload SIZ file

Choose file

Basic Options:

While solving Poisson-Boltzmann equation, use a linear or non-linear solver? (Default: Linear)

Percent of the box to be filled by molecule (Default: perfil=70)

Resolution grids/Angstroms (Default: scale=1)

Internal dielectric constant (Default: indi=4.0)

External dielectric constant (Default: exdi=80.0)

Salt concentration (Default: salt=0.15)

Relaxation parameter in non-linear iteration convergence process (Default: relpar=1.0)

Advanced Options:

Boundary conditions (Default: bndcon=2)

Convergence criteria (Default: maxc=0.0001)

Probe radius (Default: prbrad=1.40)

Maximum number of linear iterations (Default: linit=800)

Maximum number of non-linear iterations (Default: nonit=800)

Invoking Gaussian-based smooth dielectric function (Default: disabled)

The variance of Gaussian distribution (Default: sigma=2.0)

Solvation energy calculations with Gaussian-based smooth dielectric (Default: srfcut=20.0)

Invoking calculations of potential on a surface situated at a particular distance from vdW surface (Default: disabled)

Distance from vdW (Default: surfdist = 8)

Output Options:

Types of energies to be calculated (Default: All Checked)

Coulombic

Solvation

Grid Energy

Output file visualization options (Default: Potential Map)

Potential Map

Dielectric constant map

None

For technical assistance, please get in touch with delphi@g.clemson.edu. 21,684 Total views.