How to Run Delphi
To run DelPhi and analyze the results, follow the steps below:
1. Prepare three files containing:
- run parameters
- atomic radii
- atomic charges
2. Modify the Brookhaven format atomic coordinate file as necessary: e.g. if a full partial charge set on all atoms is required, it will be necessary to build in hydrogens using a suitable modeling program. Also if the output of potentials at various specified atoms is required, a second atomic coordinate file may be needed.
3. Run the program DelPhi (finite difference algorithm), in batch or interactively, directing the output into a log file if required. The log file will provide variety of energies including solvation (reaction field) energy.
4. Analyze the results. Two things that are commonly required are to read out and display the potentials. Two options exist:
- Delphi can be made to output a Biosym style potential map that can be read into Biosym's InsightII program and contoured. A utility mkcontr has been provided to facilitate this.
- Delphi potentials written in GRASP format can also be read in and displayed directly in GRASP, a companion Molecular Visualization program.
Upon installation, a directory structure should be created in order to group files in some kind of order. The directories should be arranged as:
src/ source directory
data/ atomic radii and charge data files
SOD/ protein potentials: SUPEROXIDE DISMUTASE
SPH/ test results: SPHERE
ACE/ solvation energy: ACETATE
SBT/ interaction energy: pK change in SUBTILISIN
RNA/ solvation energy, osmotic pressure, electrostatic stress and ions contribution to the fixed charges.
How to run DelPhi?
1. Running the examples:
- change the directory to the directory you want to explore (example: cd examples/ACE)
- copy *prm file into fort.10 (example: cp ace_2_1.prm fort.10)
- run DelPhi (example: type delphi and then press return. Make sure that the path to DelPhi is specified in your .login file)
- analyze the results and compare them with the provided *log file.
2. Create your own project:
- Copy *prm file from any of the examples directories to the directory in which you will run the project, file fort.10
- Modify fort.10 file by including new functions and specifying appropriate pdb, siz and crg files.
- Run DelPhi and analyze the results.