Qnifft DOCK 3.6 conversion

Revision as of 17:23, 19 October 2011 by Rgc (talk | contribs) (finished first draft?)
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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 the new phimap, you have to edit your INDOCK to point to it instead of the old phimap (rec+sph.phi usually). Once you've done that, you also have to use the new DOCK executable located in $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh The best way to use this is to use the following command instead of $mud/submit.csh:

$mud/subdock.csh $DOCK_BASE/bin/Linux/dock3.6_qnifft/dock.csh