Delphi is a program to solve the Poisson-Boltzmann equation to obtain potentials and solvation free energies for heterogenous systems.

The home page of Delphi is at
A manual of the program (pdf) is found in http:/
A similar but better manual in web format is found in

On milleotto:
module add pgi32/7.1

It is not available on the local system.

Running delphi

The program is run with the command:
delphi inputfile

if inputfile is missing, the name fort.10 is assumed.

This is a sample input file:

Three files (at least) are read in:
A pdb file (default fort.13)
An atom radii file (siz, default name fort.11)
An atom charge file (crg, derault name fort.12)

For small molecules, scale=2.0 may give very poorly converged solvation energies with errors of 29 kJ/mol for water and 54 kJ/mol for imidazoleH+. Scale=10 gives accurate results. For drug-like molecules, the error is up to 7 kJ/mol.

Moreira et al, J. Mol. Struct 729 (2005) 11 have examined the dependence of Delphi results on some parameters. They recommend the following settlings:
conv = 10^-3
perfil = 90%
scale = 2.5
coloumbic boundary conditions (bndcon=4).



The atom size file

The file can start with any number of comment lines, starting with !
Then a line defining the file format should come. It should be either (exactly for the 16 first characters:)
which gives the format
atom(a6), residue(a3), radius (f8.3)


which gives the format
atom(a6), residue(a3), residue_number(a4), subunit(a1), radius (f8.3)

Then, the rest of the file is read in this fixed format.
Blank fields are considered as wild-card characters.
No warnings are given for errors.

The atom charge file

The file can start with any number of comment lines, starting with !
Then a line is read but ignored.
The rest of the file is read in the following fixed format (same as second atom size format)

atom(a6), residue(a3), residue_number(a4), subunit(a1), charge(f8.3)

Blank fields are considered as wild-card characters.

Note that only three decimals are read for the charges (but we have changed that to six decimals)!


Note that Delphi does not interpret H-atom names in the format 1HD2 LEU correctly (i.e. as HD21), instead it is interpreted litteraly as "1HD2" and if the same name is not given in the size and charges files, a "default" charge and radii are used for those atoms, without any crash!

Use changepdb format 0.

Warning 2!

Strangely enough the program does not allow radii of 0 (as in Parse for non-polar hydrogens). If they are set to 0.1 (or even 0.001), it works. In our test case, there is no difference with an radius of 0.1 and 0.001, or even with 1.0.

 charged atom number           2radius changed from zero to    1.000000


We have not been able to run focusing calculations for big system.
The problem has been traced to the handling of phimap.

Example of a focusing file (that does not work):

Changes made to the source files

1. We decided to let the program read in specific radii and charges for all atoms. Therefore, we had to increase five parameters in the file qdiffpar5.h:

        parameter (nclist = 50000)
        parameter (nrlist = 50000)
c nrmax= maximum number of entries in radius file
        parameter (nrmax = 50000)
c ncmax= maximum number of entries in charge file
        parameter (ncmax = 50000)

2. Second, we forced the program to read 6 decimals for the charges (needed to get the correct charge on the residues with standard Amber charges):
In file rdhcrg.f, we changed the following line (from F8.3):
202     format(A6,A3,A4,A1,F11.6)

3. To read more than 10000 atoms, I changed (19/1-10) in getatm2.f:

Sample output file
  __________DelPhi V. 4 Release 1.1 ______________ 
 |                                                |
 | A program to solve the PB equation             |
 | in 3D, using non-linear form, incorporating    |
 | many dielectric regions, multisalt ionic       |
 | strength, different probe radii, periodic      |
 | and focussing boundary conditions, utilizing   |
 | stripped optimum successive over-relaxation    |
 | and an improved algorithm for mapping the      |
 | Mol. Surface to the finite-Difference grid     |
 | Recompiled on Linux and PC                     |
 |    January 2002 --------  Walter Rocchia       |
 |__________________           ___________________|
                    DelPhi V. 4                    
  program started on Mon Jan 18 2010
              at 15:19:06
 opening parameter file
 atom radii read from file
 ! Atomic radii for delphi automatically generated by WtDelph
 ! PARSE radii                                              
 reading pK style radius file
 # of radius parameter records:           3
 atomic charges read from file
 ! Atomic charges for delphi automatically generated by WtDel
 ! Amber charges from prmtop file                           
 # of charge parameter records:           3
 assigning charges and radii...
 opening formatted file:delphi.pdb
 You are not reading from an objectfile! assuming     having only molecules, and one dielectric medium
 number of atoms read in =            3
 atomic coordinates, charges and radii written to file
 Direct mapping of epsilon: (0/1)(n/y)           1
 time to read in and/or assign rad/chrg=  0.0000000E+00
 object number :              1,  is a molecule
 grid size                  :           3
 percent of box to be filled:   90.00000   
 scale,in grids/A :   1.000000   
 xmin,xmax     (A):  -9.131000      -5.777000   
 ymin,ymax     (A):  -15.74500      -12.92700   
 zmin,zmax     (A):   15.81600       19.01300   
 x,y,z range   (A):    3.354000       2.818000       3.197001   
 system geometric center in (A):  -7.454000      -14.33600       17.41450   
  grid  box is centered in (A) :  -7.454000      -14.33600       17.41450   
 object centred at (gu)     :  0.0000000E+00  0.0000000E+00  0.0000000E+00
 outer dielectric           :   80.00000   
 dielectric in medium number           1 :   1.000000   
 first kind salt concentration (M)   :  0.0000000E+00
 valences salt 1 are                   1 and           1
 second kind salt concentration (M)  :  0.0000000E+00
 valences salt 2 are                   0 and           0
 ionic strength (M)         :  0.0000000E+00
 debye length (A)           :   1000000.   
 absolute temperature (K)   :   297.3342   
 ion exclusion radius (A)   :   2.000000   
 probe radius facing water(A:   1.400000   
 probe radius, internal (A) :   1.400000   
 boundary conditions        : dipolar 
 x,y,z periodic bc. and volt. drop flags: F F F F F F
 # of linear iterations     : automatic
 # of non-linear iterations :           0
 non-linear energy calculat.: F
 manual relaxation parameter : F
 ionic direct energy contribution: F
 concentration map output   : F
 spherical charge distbn.   : F
 INSIGHT format output      : F
 site potential output      : F
 modified atom file output  : T
 map file label             :
qdiffxas: qdiffxs4 with an improved surfacing routine      
  convergence graph turned off
  potential listings turned off
 start vw surface at   0.0000000E+00
 Starting creating Vand der Waals  Epsilon Map
 Ending creating Vand der Waals  Epsilon Map
 fill in re-entrant regions at   0.0000000E+00
 boundary points facing continuum solvent=            0
 total number of boundary points before elab.=            0
 radpmax,radprb    1.400000       1.400000       1.400000   
 # of vertices =          384 # of edges =          372
 # of pairs =            3
 time to find all pairs =   0.0000000E+00
 # pairs analyzed (atom-atom and atom-object)=            3
 # exposed pairs (atom-atom and atom-object)=            3
 no. arc points  =          357
 no. surface atoms  =            3 nbur =            0
 mkacc time =   0.0000000E+00
 writing accessible surface arcs data to  ARCDAT
 grid for indexing accessible points =    1.400000   
 bgp added m=           0 bgp removed  mr =           0
 time to grow re-entrant surface =   0.0000000E+00
 no. cavity mid-points inaccessible to solvent =            0
 after surface elaboration ibnum=            0
     and               ibnumsurf=            0
 scaling boundary grid points
 time taken =   0.0000000E+00
            0 points had to be assigned by global comparison
 time to turn everything in is  0.0000000E+00
 number of charges coming from molecules            3
 number of atom coordinates read  :            3
 total number of assigned charges    :            3
 net assigned charge              :   0.0000000E+00
 assigned positive charge         :   0.8340000   
 centred at (gu) :   2.000000       1.738501       2.294499   
 assigned negative charge         :  -0.8340000   
 centred at (gu) :   1.836999       2.009001       1.801498   
 number of dielectric boundary points           0
 no. dielectric boundary points in salt =            0
 no. grid points charged and not internal=           0
 iepsmp to db, and charging done at  0.0000000E+00
 number of grid points assigned charge           1
   setting boundary conditions
  some initial phi values:
  midg,midg,1; midg,midg,igrid
   -2.721608       2.937844   
  midg,1,midg; midg,igrid,midg
    1.738883      -1.198084   
  1,midg,midg; igrid,midg,midg
   -1.356813      0.4846959   
gauss-seidel spectral radius is        0.0000000000
 estimated iterations to convergence          11
 setup time was (sec)   0.0000000E+00
 now iterating at: 15:19:07
   rms-change     max change       #iterations
   0.0000000E+00  0.0000000E+00 at          10 iterations
 finished qdiffx linear iterations
 at                       : 15:19:07
 total time elapsed so far:   0.0000000E+00
 # loops                  :           10
 mean,max change (kT/e)   :   0.0000000E+00  0.0000000E+00
 total grid energy          :        107.4648     kt
 self-reaction field energy :      0.0000000E+00 kt
 total s.charge,no epsin carrying :    0.0000
 corrected reaction field energy:   0.0000000E+00 kt
 total reaction field energy :     0.0000000E+00 kt
 All required energy terms but grid and self_react.:  0.0000000E+00kt
 energy calculations done at  0.0000000E+00
 total cpu time was (sec)   0.0000000E+00
 DelPhi exited at 15:19:07

Another ending:

 total grid energy          :        23944.70     kt
 self-reaction field energy :      0.0000000E+00 kt
 total s.charge,no epsin carrying :   16.0076
 corrected reaction field energy:   -7466.163     kt
 total reaction field energy :     -7466.163     kt
 All required energy terms but grid and self_react.:  -7466.163    kt

The interesting result (the solvation energy) is given in the line:
corrected reaction field energy:   -7466.163     kt
The conversion from kt (RT) to kJ/mol is 2.49434 kJ/mol at 300 K.


On milleotto (Samuel 2/9-09):
module add pgi32/7.1
(There are other PGI 32-bit compilors, but this was the only one that worked)

In the makefile for Delphi:

Then type make

Old stuff

The program is compiled with the Portland Group pgf77 and pgcc compilers.
It runs on docenten.

On docenten:
Files are in /sw/pkg/bio/DELPHI/DELPHI_2004_LINUX
module add pgi32/5.2

On toto7/wheinim64
Files are in /sw/bio/DELPHI/DELPHI_2004_LINUX.
module add pgi/5.2

Older (for docenten; Jacob, 30/1-08):
Change in makefile

make delphi

On docenten in


You will find a correctly compiled version (intel) and the makefile.

Remember to

module add intel32

before typing


I like the intel compiler which is the main reason for chosing this. It can be shiftet to f.ex. pgf by using the old makefile and

module add pgi

and chosing a 32 bit compiler as well in this case.