Qnifft DOCK 3.6 conversion

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Qnifft is a new option for use instead of DelPhi with DOCK 3.6 It is a poisson boltzmann solver program from Kim Sharp [[1]]. It has been integrated into the DOCK Blaster and DOCK 3.6 toolchain. For now if you make use of it, please cite:

Sharp, K. A. 1995. Polyelectrolyte electrostatics: Salt dependence, entropic and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model. Biopolymers 36:227-243. 10.1002/bip.360360210


Gallagher, K., and K. A. Sharp. 1998. Electrostatic Contributions to Heat Capacity Changes of DNA-Ligand Binding. Biophys. J. 75:769-776.http://dx.doi.org/10.1016/S0006-3495(98)77566-6

Using the new code

A compiled qnifft binary is in $DOCK_BASE/bin/Linux/qnifft22_193_pgf_32

Running qnifft requires setting your $DELDIR environment variable to $DOCK_BASE/src/qnifft

The default way to run qnifft is to copy the qnifft.parm file from $DELDIR and run it by calling

qnifft qnifft.parm

If you're using DOCK Blaster, you can make the new electrostatic grids by typing:

make grids/rec+sph.qnifft.phi

or if you want to use the full DOCK Blaster toolchain you can type

make autonew

Once you have