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DelPhi (Feb. 1995 release)

DelPhi is a program which solves the Poisson-Boltzmann equation by a grid based method using an optimized successive over-relaxation algorithm. The Poisson-Boltzmann equation can be used to model the effect of the dielectric differential between vacuum and water or any other solvent whose dielectric is known. The effects of ionic strength is incorporated through the (non)linear Poisson-Boltzmann equation. Periodic Boundary Conditions (PBC) can be used. The output from the program can be used to calculate interactions, changes in pKa, solvation energies and other properties of interest. Potentials may be displayed as 3-D isopotential contours, 2-D slices or as color coded molecular surfaces in GRASP. Delphi uses units of temperature for all energies it calculates. A convenient conversion factor to convert that to kcal/mol is 0.59

Availability

Available on all SGI machines. No user setup is required.

Software Usage

There are two variants of the program. "delphi" has an upper limit of 65 on no. grids used to partition the box. (adequate for small molecules, peptides and small proteins (<50 residues). "DELPHI" has has an upper limit of 129 on no. grids used to partition the box and should be used for larger systems.

Once you've decided which version you wish to run, build your parameter file. The Delphi program needs four files - a structure file in the PDB format (file.pdb) - a size file (file.siz) which contains the van der Waals radius for all atoms in the sequence it occurs in the PDB file - a charge file (file.crg) which contains the atomic charges in the same sequence - and a .prm file which is the command line options file for Delphi to use during runtime. BioGraf version 330 - msc or save - has an option in the In/Out menu to write these out automatically.

There are several choices to be made for the van der Waals size file. The one implemented in BioGraf is based on the optimized PARSE parameters published by Barry Honig's research group at Columbia. However, it is rather limited in its implementation. SDG has extended some of the size cases from the original Pauling set that the PARSE was based on. The problem with the extended cases is there are no adequate charges available for this. The second possibility for sizes is to use the Dreiding parameters. The BioGraf In/Out menu will not do this yet, but one can edit the PARSE sizes and change them to BioGraf. PS-GVB uses yet another set of sizes that work best with QM Potential Derived Charges.

For the charges there are several choices also. The BioGraf interface currently will write whatever the charges are on the molecule (either from the .bgf file or edited on screen or QEq). The PARSE papers from Honig have provided charges for some of the common protein polar functional groups, but not others are not present. Halogens for example are not available. Mamadou Diallo is investigating the QEq charge scheme, but results are not available at the present.

Examples of these different files are below:

------ file: phenol.pdb ------
HEADER PHOL                                                                
REMARK Created by sdg @ sgi1 on 11/22/95   11:18:45                        
HETATM    1 C_1  ORG A   1       5.303   1.975  -8.522
HETATM    2 C_2  ORG A   1       6.628   1.949  -8.089
HETATM    3 C_3  ORG A   1       7.338   0.749  -8.089
HETATM    4 C_4  ORG A   1       6.724  -0.423  -8.522
HETATM    5 C_5  ORG A   1       5.399  -0.398  -8.955
HETATM    6 C_6  ORG A   1       4.688   0.801  -8.955
HETATM    7 H_1  ORG A   1       4.752   2.905  -8.522
HETATM    8 H_2  ORG A   1       7.100   2.861  -7.754
HETATM    9 H_3  ORG A   1       7.279  -1.350  -8.520
HETATM   10 H_4  ORG A   1       4.924  -1.309  -9.291
HETATM   11 H_5  ORG A   1       3.662   0.821  -9.291
HETATM   12 O_1  ORG A   1       8.638   0.718  -7.665
HETATM   13 H_6  ORG A   1       8.897   1.604  -7.406
CONECT    1    2    6    7
CONECT    2    1    3    8
CONECT    3    2    4   12
CONECT    4    3    5    9
CONECT    5    4    6   10
CONECT    6    1    5   11
CONECT    7    1
CONECT    8    2
CONECT    9    4
CONECT   10    5
CONECT   11    6
CONECT   12    3   13
CONECT   13   12
END

----- file:  phenol.siz --------
! default extended atom radii based loosely
! on mike connolly's MS program- note H's are 0
atom__res_radius_color_
C_1       1.7000
C_2       1.7000
C_3       1.7000
C_4       1.7000
C_5       1.7000
C_6       1.7000
H_1       1.0000
H_2       1.0000
H_3       1.0000
H_4       1.0000
H_5       1.0000
O_1       1.4000
H_6       1.0000

---- file: phenol.crg -----
! full charges on side chains and termini only
atom__resnumbc_charge_
C_1   ORG      -0.127
C_2   ORG      -0.088
C_3   ORG       0.281
C_4   ORG      -0.026
C_5   ORG      -0.144
C_6   ORG      -0.112
H_1   ORG       0.118
H_2   ORG       0.096
H_3   ORG       0.137
H_4   ORG       0.116
H_5   ORG       0.122
O_1   ORG      -0.702
H_6   ORG       0.329

--------file: phenol.prm ----------
grid size =65
prbrad=1.4
perfil=80
indi=2
exdi=1
bndcon=2
salt=0.0
in(pdb,file='phenol.pdb')                                                
in(siz,file='phenol.siz')                                                
in(crg,file='phenol.crg')                                                
energy(s)

Invoke the program as in one of these examples (substituting your own parameter file):

% delphi phenol.prm
or,
% DELPHI phenol.prm
The first calculation has the external dielectric (exdi=) set to 1 for vacuum. Now change this to the value for your solvent of interest (80 for water) and run the case once more. To get the true solvation energy, subtract the vacuum value from the solvent value.

Documentation

Documentation for the latest version is available online from Columbia University. You can view the Delphi home page and the DelPhi I/O Documentation

Usage Assistance

Siddharth is the most experienced user.

Old Version V3.0

The previous version of Delphi (V3.0) is still available for the time being. If you discover that you the old version does something that you cannot do with the new version then let DLW know (with an explanation) so that he doesn't remove the old version without notice.

Here is the information from the previous version:

DelPhi (V3.0)- A Macromolecular Electrostatics Modelling Package -
has been installed on sgi1.

The abstract extracted from the manual is included below:

        DelPhi is a software package which calculates  electrostatic
        potentials in and around macromolecules. It incorporates the
        effects of ionic strength through the  (non)linear  Poisson-
        Boltzmann  equation.   Any value for the dielectric constant
        of the molecule and  solvent  may  be  specified.   Periodic
        boundary  conditions  can  be  used  to  model long periodic
        energies and many other properties of interest.   Potentials
        may  be displayed as 3-Dimensional isopotential contours, 2-
        Dimensional contour  slices  or  as  color  coded  molecular
        surfaces

The user's manual is in the file /exec/delphi/docs/delphi.rno
A hard copy is shelved in 056c, and one is on the top shelf of
Siddharth's bookshelf.


The executables are in /exec/delphi/bin.  You may want to add this
to your path variable within your .cshrc file.

Before running, you should also add the following line to your .cshrc file:

 setenv DELDIR /exec/delphi



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Last Modified $Date: 95/12/13 16:21:21 $ by $Author: dlw $
Problems or suggestions should be reported to sysmgr@wag.caltech.edu