Introduction
This is an initial attempt at a Java software implementation of the SSIP method as described in the paper "Footprinting molecular electrostatic potential surfaces for calculation of solvation energies".
Specifically, the footprinting aspect of the calculation will be initially worked upon here since a Java QM solution does not exist at the moment. For the moment, the QM aspects will be dealt with by NWChem.
Compiling from Source
This will compile and install the SSIP tools to the Debian based OS.
Debian Stretch / Ubuntu Trusty / Ubuntu Xenial Debian package
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Install the needed packages and configure Java.
sudo apt-get install git maven openjdk-8-jdk
sudo update-alternatives --config java sudo update-alternatives --config javac
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Clone, build and install.
git clone https://bitbucket.org/mjw99/ssip.git cd ssip ; mvn clean package ; sudo dpkg -i ./ssip-/target/.deb
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Check command line output.
SSIP Code:
ssip - A tool for footprinting molecular electrostatic potential surfaces
http://dx.doi.org/10.1039/C3CP53158A
Git version: develop e608f92
Option Description
------ -----------
-?, -h, --help display this output
-c, --cml <String> the CML file of the corresponding molecule in the cube
file.
-i, --isout <String> the isout file that has been generated using the QM tool
--legacy this switches to the legacy mode, allowing the use of an
isout file and pdb.
-m, --cube <String> the cube file for the MEPS corresponding to the molecule,
generated by the QM tool.
-n Function in a non-interactive mode.
-p, --pdb <String> the PDB file of the corresponding molecule in the isout
file
-v Visualise SSIP surface.
-w <String> write the files to file.
Example usage:
ssip --legacy -i /usr/share/ssip-repo/ExampleData/benzene_001_0.002_0.00003.isout -p /usr/share/ssip-repo/ExampleData/benzene_001_new.pdb
ssip -m /usr/share/ssip-repo/ExampleData/XLYOFNOQVPJJNP-UHFFFAOYSA-N_0.0020_merged.cube -c /usr/share/ssip-repo/ExampleData/XLYOFNOQVPJJNP-UHFFFAOYSA-N.cml
Phase transfer code:
phasetransfer - A tool for calculating free and bound concentations and free energies of transfer
Git version: phasetransfer e8bbd7b
Option Description
------ -----------
-?, -h, --help display this output
--calc option sets it to calculate new concentrations
for the phases, otherwise they are read in.
--concentrationUnit <String> concentrationUnit (default: MOLAR)
-e, --energies [String] output the free energies (default: all)
-o, --outputfile <String> output file name, required
-p, --phaseOut output the phase states from the calculation to a
PhaseCollectionList
--phaseCollection phase collection in input file
--phaseCollectionList phase collection list in input file.
--phaseFile <String> phase input file name
--solute <String> solute file name
--solvent <String> solvent file name
-t, --temperature <Double> temperature value (default: 298.0)
--temperatureUnit <String> temperatureUnit (default: KELVIN)
Example usage:
phasetransfer -p -o phaseOutFile.xml --solute /usr/share/ssip-repo/phasetransfer/ExampleData/watersolute.xml --solvent /usr/share/ssip-repo/phasetransfer/ExampleData/waterphasesolvent.xml
phasetransfer -e -o energyOutFile.xml --solute /usr/share/ssip-repo/phasetransfer/ExampleData/watersolute.xml --solvent /usr/share/ssip-repo/phasetransfer/ExampleData/waterphasesolvent.xml
Debian Stretch / Ubuntu Trusty / Ubuntu Xenial standalone jar
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Repeat the steps above, but build using
mvn clean compile assembly:single
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Execute using
java -jar ./ssip-footprint/target/ssip-foorprint-2.2.0-SNAPSHOT-jar-with-dependencies.jar java -jar ./ssip-phasetransfer/target/ssip-phasetransfer-2.2.0-SNAPSHOT-jar-with-dependencies.jar