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.prmor,
% DELPHI phenol.prmThe 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.
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