PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc.
pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions.
Perl extensions for working with chemical information, for example SMILES strings, molecular file formats, creation of VRML files, conversion to internal coordinates. See also PerlMol.
PINY_MD is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based simulations on system ranging in complexity from simple molecular liquids and crystals to large biomolecular systems. In addition, PINY_MD can perform ab initio molecular dynamics and geometry optimization using plane-wave based generalized gradient (GGA) density functional based representations of the electronic structure combined with the Car-Parrinello propagation scheme.
PLATON is a versatile SHELX97 compatible multipurpose crystallographic tool. Most PLATON features complement those available in the excellent and widely distributed SHELX97 package for crystal structure determination and refinement.
POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases).
PovChem is a chemical visualisation and illustration program with a graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration, then exports the picture in POV-Ray format (high-quality images).
PQS (Parallel Quantum Solutions) Ab Initio Module is a comprehensive program for electronic structure calculations. All major ab initio functionality is fully parallel.
ProtoFit is a tool for optimization of surface protonation models from acid-base titration data. Although ProtoFit is designed with the analysis of the proton buffering behavior of surfaces in mind, it can be used equally well for other substances such as a dissolved acids that reversibly exchanges protons with water.
PWscf (Plane-Wave Self-Consistent Field) is a set of programs for electronic structure calculations within Density-Functional Theory and Density-Functional Perturbation Theory, using a Plane-Wave basis set and pseudopotentials.