Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_71 DELPHI Program at MUSC.
 DELPHI II

A program to solve the PB equation             
in 3D, using non-linear form, incorporating    
2 dielectric regions, ionic strength, 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.   

Running the program DELPHI is easy but you will need at least four files.
These are:


*.pdb a PDB format molecular coordinate file Get 1FVA from RCSB.
*.prm a parameter file to control DELPHI
*.siz a size file detailing various ionic radii
*.crg a charge file for metal ions and various side chains


The siz and crg files may be re-used from PDB file to PDB file
as long as the ions in the structure are listed in the file. The 
examples above may be useful starting points. The prm file
will need customization. The example prm file is set up to
write a DELPHI potential to GRASP format. The output "phi"
file and the PDB file would then be read into GRASP to produce
a graphic.

Running DELPHI would require that you type

 delphi filename.prm > filename.log & 

Be sure to consult the DELPHI Manual 
and note the examples above. Here's a jpg of the results (1FVA.phi from delphi and
1FVA.pdb are loaded into GRASP in order to create this image) based on the files  
used in the above examples.




Good Luck!

   
 

The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
Last modified: June 5, 2001- ESH

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