Application Index

Programs and scripts to read, write, or convert molecular structure and trajectory files. This includes both standalone programs as well as add-on packages for systems such as Matlab and Mathematica.

FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm, and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another. FixDCD is a tiny utility to modify the header of an X-PLOR DCD file to make it readable by programs expecting Charmm DCD files, at the expense of a Timestep size value in the header.
View Application Entry for FlipDCD

Intocham takes an InsightII .car file as an input and, using the atom type information and atom-atom distances generates a full suite of topology, parameter and coordinate files for either Charmm, Amber or Moil.
View Application Entry for Intocham

Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to : Postscript (.ps), Adobe Illustrator (.ai), Scalable Vector Graphic (.svg), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language (.hpgl), xfig file (.fig), gif image file(.gif), PBM Portable aNy Map file (.pnm).
View Application Entry for Treeplot

AutoZmat is a program which converts between file formats. It automates a generation of Z-matrix for BOSS, MCPRO, GAUSSIAN, MOPAC, JAGUAR, etc. The algorithm used here is a breadth-first search method in the graph theory with criteria in such a way that improper torsions are handled efficiently. Alternatively, Z-matrix can be built using a template Z-matrix. Hydrogen atoms can be added to vacant valencies to C, N, O, and S.
View Application Entry for AutoZmat

AmberFFC has been designed to convert the different existing AMBER force fields (FF) freely available in the public domain (Kollman group, http://www.amber.ucsf.edu), for use with commercial molecular modeling packages, using the Molecular Simulations Inc. (MSI, San Diego, http://www.msi.com) software package as a case model. In its current version, AmberFFC can convert six AMBER FF for the MSI modeling package. The program is free for all academic users after signing a license.
View Application Entry for ADF AmberFFC

This is a free program which make VMD more useful but is not part of the VMD distribution. Conect2psf converts the CONECT records from a PDB file into a PSF file so the bonds are displayed properly in VMD. Of course, you do not want to use the PSF for a real simulation as the rest of the bonding information is not present. Notes: Only a binary for IRIX 5.x is available at the present time.
View Application Entry for Conect2psf

Presents and converts the file formats used by the major PC modeling programs. In this new release more than 30 different molecule files are supported.
View Application Entry for Mol2Mol

A file conversion program for data formats of molecular structures in chemistry MOLCONV was renewed. The aim of MOLCONV is applied in dealing with various data formats with flexibility. A macro-language and its interpreter for file conversion procedures are employed for this purpose. The new MOLCONV was provided with only conversion function for an independent program, at first. The old was one of the applications, which consisted of structure input, display, etc., for chemistry. Secondly, in addition to the conventional way of step by step depending on menu selection, the way of a command line procedure was adopted in the new program. At last the interpreter was fortified.
View Application Entry for Molconv

mmCIF is a set of tools for handling the Macromolecular Crystallographic Information File format.
View Application Entry for mmCIF

Catdcd functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use catdcd to write only selected atoms to the final DCD file.
View Application Entry for CatDCD

PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc.
View Application Entry for PDBCat

Trio is a conversion program that provides the ability to read and write molecular dynamics trajectory files in several common formats. It is a small standalone program, and should be easy to compile and run on almost any system.
View Application Entry for Trio

MatDCD: a DCD reader for Matlab Written by Justin Gullingsrud, based on the DCD code in VMD *supports Charmm and xplor-format DCD files *can read both big- and little-endian storage formats *can specify which atom indices to load; no need to load entire file *Does not support dcd files with fixed atoms
View Application Entry for MatDCD

Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. It can add or delete hydrogens from any file format. It can assign hybridization, bond order, and connectivity when these elements are not present in the input file. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0.
View Application Entry for Babel