Difference between revisions of "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 [[http://crystal.med.upenn.edu/software.html]]. It has been integrated into the [[DOCK Blaster]] and [[DOCK 3.6]] toolchain. For now if you make use of it, please cite:
 
Qnifft is a new option for use instead of DelPhi with DOCK 3.6 It is a poisson boltzmann solver program from Kim Sharp [[http://crystal.med.upenn.edu/software.html]]. 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. [http://10.1002/bip.360360210 10.1002/bip.360360210]
+
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. [http://dx.doi.org/10.1002/bip.360360210 10.1002/bip.360360210]
  
 
and  
 
and  
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make autonew
 
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:
+
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/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
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  $mud/subdock.csh $DOCK_BASE/bin/Linux/dock.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
 +
 
 +
parameter (nsize=179)
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 +
to
 +
 +
parameter (nsize=193)
 +
 
 +
Then you have to run
 +
 
 +
cd i386 ;  make clean ; make ; make SIZE=32
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 +
To produce new binaries for use with these grids.
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 +
== INDOCK file ==
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delphi_file            ../../grids/rec+sph.qnifft.phi
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delphi_nsize        193
 +
 
 +
== 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.
 +
 
 +
[[Category:DOCK]]

Latest revision as of 20:32, 8 October 2012

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

and

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/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/dock.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

parameter (nsize=179)

to

parameter (nsize=193)

Then you have to run

cd i386 ;  make clean ; make ; make SIZE=32

To produce new binaries for use with these grids.

INDOCK file

delphi_file             ../../grids/rec+sph.qnifft.phi
delphi_nsize         193

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.