DelPhi

Contents

Release 2000, February 2000

1. Introduction

What is DelPhi?

Hardware

Installation

About This Manual

Starting DelPhi-Insight

The DelPhi Calculation

The Solvation Calculation

Starting DelPhi - Standalone

2. Theory and Application

Models

Poisson-Boltzmann equation

Finite Difference Approximation

Electrostatic Potential

Total Electrostatic Energy

Reaction Field Energy

Total Solvation Energy

Simple Solvation Models

Generalized Born Model

DelPhi-Based Model

Free Energy of a Transfer From Water to Octanol

Conformational Energies in Vacuum and Solution

DelPhi Implementation

Limitations of the Model

Solvation Implementation

1. DelPhi-based calculation

2. Other solvation models

3. DelPhi-Insight Command Summary

Setup Pulldown

Run_DelPhi Pulldown

Potential Pulldown

Templates Pulldown

Grid Pulldown

Contour Pulldown

4. DelPhi-Insight Methodology

Basic Steps for a DelPhi Calculation

Step 1: Defining the Molecule

Step 2: Creating Charge and Radius Template Files

Charge Templates

Radius Templates

Step 3: Setting up the Calculation Parameters

Defining the Solute

Defining the Solvent

Defining the Calculation Grid

Setting Iterations

Setting Boundary Conditions

Output File Specification

Calculating Energy Values

Initializing Parameters

Listing the Current Setup Parameters

Step 4: Performing the DelPhi Calculation

Step 5: Analyzing the Results

Site Potential Output (.frc)

Difference Grids

Displaying Potential Grids

DelPhi Calculation Strategies

Examination of Potential Contours around a Molecule

Electrostatic Solvation Energy

Reaction Field Energy

Site-Directed Mutations and Change in pK

5. Tutorials

Pilot Online Tutorials

6. DelPhi-Standalone Command Summary

DelPhi Calculation Parameters

Grid Definition

Menu Entries 1-3

Grid Center -- Menu Entry 1

Grid Resolution -- Menu Entry 2

Grid Size -- Menu Entry 3

Interior Dielectric --Menu Entry 4

Exterior Dielectric -- Menu Entry 5

Ionic Strength -- Menu Entry 6

Ion Exclusion Radius -- Menu Entry 7

Probe Radius -- Menu Entry 8

Boundary Condition -- Menu Entry 9

Periodic Bounds (X,Y,Z) -- Menu Entry 10

Linear P-B Iterations -- Menu Entry 11

Non-linear Iterations -- Menu Entry 12

Concentration Flag -- Menu Entry 13

Spherical Charges -- Menu Entry 14

Files: GRD,FRC,ATM,EPS, SRF, SCH-- Menu Entry 15

Energies (total,react,coul) -- Menu Entry 16

Spectral Radius and Convergence Params -- Menu Entry 17

File Header -- Menu Entry 19

User Interface

Parameter Menu

Input File Menu

Selecting a Charge File

Charge File Editor

Radius File Menu

Leaving the Input File Menu

Job Submission Menu

7. DelPhi-Standalone Methodology

The DelPhi Calculation

Analyzing the Results

Utility Programs

8. DelPhi-Standalone Tutorials

Introduction

Before You Start...

LESSON 1: Calculation and Display of Potential Maps

Objective

Setting Up the DelPhi Calculation

LESSON 2: pK Shift in Subtilisin

Objective

Notes

LESSON 3: Solvation Energy of Acetate Ion

Objective

Notes

Discussion

9. Solvation Command Summary

Setup Pulldown

Solvation_Run Pulldown

Background_Job Pulldown

Forcefield Pulldown

10. Solvation Methodology

Step 1: Defining the Molecule:

Step 2: Choosing the Model and Setting up the Input Parameters

Defining the Model

Choosing the Accuracy Level

Step 3: Performing the Solvation Calculation

Setting Up the Background Job

Starting the Job

Monitoring a Background Job

Step 4: Analyzing the Results:

11. Tutorials

Pilot Online Tutorials

A. Installation

Silicon Graphics Installation

B. Utilities

contour2d

Main Menu

Parameter Menu

Potential Menu

Surface Menu

epstogrd

format_phi

unformat_phi

addmap

crgedt

radedt

C. References

D. Bibliography

E. File Formats

Input Files

Molecular Coordinate File (default file extension *atm)

Potential Parameter File (default file extension *.prm)

Charge File (default file extension *.crg)

Important Notes

Atomic Radius File (default file extension *.siz)

Potential Map For Focussing (optional file: default file extension *.grd)

Output Files

Log file (default file extension *.log)

Dielectric Map (optional file: default file extension *.eps)

Potential Map (default file extension *.grd)

Site Potential Output file (optional file: default file extension *.frc)

File Formats

Description of File Formats

file.pdb

file.atm

file.car

file.prm

file.crg: Charges to be assigned to each atom/residue/#/chain type.

file.siz: van der Waals radii to be assigned to each atom/residue type

file.frc: list of potentials and fields at coordinates in *.pdb file

file.grd: potential map in Insight format

file.eps: dielectric map

file.kt: file of contour levels used by contour2d and contour3d

DelPhi Library Files

default.prm (Default_Params)

default.siz (DelPhi_Defaults)

insight.siz (VDW_Radii)

prot_full.crg (Protein_Formal)

biosym_full.crg (CVFF_Formal)

prot_back.crg (Protein_Backbone)

prot_amb.crg (Protein_Amber)

nuca_full.crg (DNA_RNA_Formal)

nuca_amb.crg (DNA_RNA_Amber)

Solvation Input Files

cff91.siz

parse.siz