Qnifft DOCK 3.6 conversion
Qnifft is a new option for use instead of DelPhi with DOCK 3.6 It is a poisson boltzmann solver program from Kim Sharp []. 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
If you're using DOCK Blaster, you can make the new electrostatic grids by typing:
or if you want to use the full DOCK Blaster toolchain you can type
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:
This should produce compatible OUTDOCK & test.eel1.gz files.
Recompiling DOCK 3.6 to use the new Qnifft grids
If you're using a different version of DOCK 3.6 and want to change it to be compatible with Qnifft-produced grids, you only have to change one line. In max.h change
Then you have to run
cd i386 ; make clean ; make ; make SIZE=32
To produce new binaries for use with these grids.
Backwards compatibility with the old grids
Edit your INDOCK file, add a delphi_nsize parameter and set it to 179. This allows use of old delphi grids instead of the 193 sized Qnifft grids.