Free pdb software for linux

pbd is a simple database management system for PHP programs.

This DBMS can be used to create a Web site that dynamically stores data even if you cant afford a Web hosting service that offers MySQL.

pdb is simple and easy to use.

Packet Debugger presents a debugger-like UI for pcap packet capture files.

The Packet Debugger (pdb) allows users to work with packet streams as if they were working with a source code debugger.

Users can list, inspect, modify, and retransmit any packet from captured files, as well as work with live packet captures.

spsim is a simple program that tries to realistically simulate the diffraction pattern of an input PDB recorded on a CCD with specified characteristics.

spsim takes a PDB as input and outputs noise-free and realistic diffraction patterns according to the experimental conditions chosen by the user.

Installation:

To install simply download the source code, extract it go to the libconfig directory, run configure and make, go to the parent directory and run make. For more information please check the included documentation.

Mindy is a very simple, serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files. The program is written in very straightforward C++.

Installation

Unpack the distribution. A directory named "mindy" will be created. In the mindy directory are two subdirectories, "src" and "test". The "src" directory contains the source code and a Makefile to build mindy.

Typing "make" within the src directory shoud build mindy using g++. If you would like to build mindy using a different compiler or different compiler flags, use one of the build targets in the Makefile or add a new one.

The executable is named mindy_$ARCH, where ARCH is the platform. by default, this is "g++".

Using

The command line syntax for mindy is:

mindy nsteps pdbfile psffile paramfile

Nsteps specifies how many timesteps to take. pdbfile and psffile are the coordinate and structure files, respectively, of the system you want to simulate. paramfile is the name of your parameter file. Both the psf file and the parameter must be in X-Plor format.

The test directory contains two sets of files which can be used as inputs for mindy. "alanin" is a 66 atom polypeptide, and "brH" is a crystal structure of bacteriorhodopsin containing 3762 atoms. Run alanin by typing

mindy 1000 alanin.pdb alanin.psf alanin.params

at the command line.

Open Babel project is designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
Main features:
- A huge variety of common chemical file formats, including SDF/MOL, Mol2, PDB, SMILES, XYZ, CML... (details)
- Recognition of file type based on filename extension
- Chemical MIME support
- SMARTS matcher
- Flexible atom typer
- Flexible bond typer for perception of multiple bonds from atomic coordinates
- Gasteiger partial charge calculation
- Hydrogen addition and deletion
- Isotope support, calculation of average and exact masses
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Multiple conformer storage within molecules
- Command line conversion for multiple molecules in one file
- Command line interface
- Bitvector class
- Vector and matrix transformations
- Molecular test suite
- Open-source/Free Software under the GNU General Public License
- Cross platform (Windows, Linux, Mac OS X, SGI, Solaris, Dreamcast...)
Version restrictions:
- Generate coordinates for SMILES strings. (Meaning all coordinates will be zero when converting from a SMILES string.)
- Handle 2D->3D conversion (or vice versa).
- Handle a variety of important file formats.
Whats New in 2.1.1 Development Release:
- Improved scripting support, including dictionary-support for OBGenericData in pybel, casting from OBUnitCell, etc. Improved access to OBRings from OBMol.GetSSSR().
- Added support for descriptors (e.g., PSA, logP) from scripting interfaces.
- Added support for reading all PDB records (beyond current atom and bond connections). Records not handled directly by Open Babel are added as key/value pairs through OBPairData.
- Added a new configure flag --with-pkglibdir to allow Linux package distributors to define version-specific directories for file format plugins.
- Fixed a bug which would not output chirality information for canonical SMILES with 3D files.
- Fixed problems with new line-ending code. Now correctly reads DOS and old Mac OS files with non-UNIX line endings.
- Correctly rejects SMILES with incorrect ring closures. Thanks to Craig James for the report.
- Fixed a crash when output to canonical SMILES.
- Fixed a crash when converting from SMILES to InChI.
- Fixed a crash when reading some PDB files on Windows.
- Fixed a crash when reading invalid MDL/SDF files.
- Fixed a bug which made it impossible to read some GAMESS files.
- Fixed a problem when reading ChemDraw CDX files on Mac OS X.
- A large number of additional fixes, including some rare crashes.

This program places the required number of sodium ions around a system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex).

The ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy:

Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|

All the constants are dropped out from this formula, resulting in some weird energy units; that doesnt matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations.

The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage.

It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.

PyMOlyze project can analyze the results of quantum chemistry (DFT) calculations. Gaussian 03 and Jaguar 6.0 files are supported.
The following analyses are available for user-defined molecular fragments:
- Mulliken Population Analysis (MPA)
- C-squared Population Analysis (SCPA)
- Density of States (DOS) plots
- Overlap Population Analysis
- Overlap Population DOS
PyMOlyze was inspired by AOMix, which is a console-based, Windows-only program that has features including (and in addition to) those listed above. I wrote PyMOlyze because I wanted a user-friendly Linux program to do MPA for each molecular orbital of Gaussian calculations. If PyMOlyze doesnt address your needs, check out AOMix (or shoot me an email and well talk).
Python, the python extensions to Qt and Qwt (PyQt and PyQwt), and some C++ functions (for speed optimizations) were used to create PyMOlyze; therefore it should run on pretty much any modern platform with minor modifications. It has only been tested on Windows XP, Windows 2000, and Gentoo Linux, but there is no reason for it not to be supported on any platform with python, PyQt, and PyQwt available.
Enhancements:
- OpenGL 3D rendering
- Atom is highlighted in 3D when choosing an atom/orbital for population analysis
- Observe structural changes during an optimization
- Cartesian coordinate editor (any step of the optimization)
- Functions for translating or rotating a molecule
- Center molecule on an atom
- Rotate molecule so that two atoms are along an axis
- Rotate moelcule so that three atoms lie in a plane
- Save structures as XYZ, PDB, internal coordinates, etc.
- Charge Decomposition Analysis (using the method developed by Frenking et al.)
- Fragment Analysis to study bonding interactions by determining contributions of fragment MOs to molecular MOs