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... the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications.
http://www.nanoengineer-1.net
http://www.ime.unicamp.br/~martinez/packmol/
http://lammps.sandia.gov/
Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neuralnet library, Hooke-Jeeves global optimizer, and misc. math & statistics.
UPDATE:
The latest version of NNScore1 can be found here: http://git.durrantlab.com/jdurrant/nnscore1
The latest version of NNScore2 can be found here: http://git.durrantlab.com/jdurrant/nnscore2
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NNScore is a scoring function for characterizing the potency of receptor-ligand complexes. It is based on neural networks, computational models that simulate the microscopic organization of the brain.