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README.md

DelphiPka v2.3

Delphi-PKA is a DelPhi-based C++ program, allowing to predict pKa's for ionizable groups in proteins, RNA and DNA. Unique approach stems from:

  1. Use gaussian-based smooth function to mimic conformational changes associated with ionization changes.
  2. Calculate the electrostatic energy without defining molecular surface.

Our web server: http://compbio.clemson.edu/pka_webserver/

For questions and help, visit http://compbio.clemson.edu/forum/ or email to delphi@g.clemson.edu

Running DelphiPka on a PC

Compile DelphiPka

To compile the source code, you will need following library:

C++ compiler needs to be 4.4 or higher, which includes C++11 feature.

With all the required above, run:

make

For the users that do not want to compile MPI version:

Edit src\delphiPKa\prime_environment.h:

And delete two lines #define MPI_PARALLEL and #include <mpi.h>.

Then change the CC entry in Makefile to g++ or clang++

If you want to build the static version, you can modify the Makefile, and add -static in CFLAGS entry and LDFLAGS entry (only support without MPI).

Running DelphiPka on Palmetto HPC

With PBS script (Recommend)

# login to the palmetto HPC login node
git clone https://github.com/delphi001/DelphiPka.git
# upload your pdb file
cd DelphiPka
# modify the run.prm and sample.pbs
qsub sample.pbs

The pbs script will claim the computing node, setup the environment, build the program, and run the delphipka automatically. This script will run with 8 core by default. To change the cpu number, and memory size, you can modify the sample.pbs file.

Build the program on Palmetto HPC, and run it manually

You need to load the following modules on Palmetto first:

  • gcc/4.8.1
  • openmpi/1.6.4
  • gsl/1.16
# claim a computing node
# Recommend flag: select=1:ncpus=8:mem=40gb:mpiprocs=8:interconnect=fdr,walltime=72:00:00
module purge
module add gcc/4.8.1 openmpi/1.6.4 gsl/1.16
git clone https://github.com/delphi001/DelphiPka.git
cd DelphiPka
make -j8

mpirun --mca btl openib,self --mca btl_openib_warn_nonexistent_if 0 -np 8 bin/delphiPKa run.prm

How to change config file

Steps:

  1. Open the run.prm and edit pdb name entry, charge and radius parameter entries with your desire. Currently supports amber, charmm22 and parse parameters.
  2. For other entries, ref the manual and edit with your own desire.
  3. Change the sample.pbs to your desired job name. And qsub the pbs script.