sci-chemistry / pdbmat

Calculate Tirion's model from pdb structures

Official package sites : ·

A fortran program in which Tirion's model (also called the Elastic Network Model) is implemented. Within the frame of this model, atoms (particles) less than cutoff (angstroms) away from each others are linked by springs of same strength. Alternatively, a list of interacting atoms can be given to the program. Requirements: a file with the coordinates of the system, in PDB (Protein Data Bank) or "x y z mass" format. Output: the hessian (the mass-weighted second derivatives of energy matrix), in the "i j non-zero-ij-matrix-element" format. Diagstd, a fortran program with a standard diagonalization routine, can next be used in order to obtain the corresponding normal modes of the system. If the system is large, the RTB approximation can prove usefull (see below).

v3.89-r1 :: 0 :: gentoo

~amd64 ~amd64-linux ~x86 ~x86-linux
USE flags


Install examples, usually source code

virtual / fortran : Virtual for Fortran Compiler

virtual / fortran : Virtual for Fortran Compiler

sci-chemistry/pdbmat-3.89-r1 - -- Configuring incomplete, errors occurred!
Repository mirror & CI · gentoo
Merge updates from master
Sam James · gentoo
sci-chemistry/pdbmat: port to EAPI 8
Closes: Closes: Signed-off-by: Sam James <>
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <>
Johannes Huber · gentoo
sci-chemistry/pdbmat: EAPI 6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <> X-Thanks: Alec Warner <> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <> - validation scripts X-Thanks: Patrick Lauer <> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed