Gentoo Packages

Search

Install

Install this package:

emerge -a sci-chemistry/pdbmat

If the package is masked, you can unmask it using the autounmask tool or standard emerge options:

autounmask sci-chemistry/pdbmat

Or alternatively:

emerge --autounmask-write -a sci-chemistry/pdbmat

Package Information

Description:

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).

Homepage:

http://ecole.modelisation.free.fr/modes.html

License:

CeCILL-2

Versions

Metadata

Description

• 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).

Maintainers

• Gentoo Chemistry Project (sci-chemistry@gentoo.org) - Type: project

<pkgmetadata>
	<maintainer type="project">
		<email>sci-chemistry@gentoo.org</email>
		<name>Gentoo Chemistry Project</name>
	</maintainer>
	<longdescription>
  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).
  </longdescription>
</pkgmetadata>

Lint Warnings

• [Warning] USE flag 'examples' in ebuild 3.89-r1 is not documented in metadata.xml
• [Error] Missing md5-cache for ebuild pdbmat-3.89-r1

USE Flags

Manage flags for this package: euse -i <flag> -p sci-chemistry/pdbmat | euse -E <flag> -p sci-chemistry/pdbmat | euse -D <flag> -p sci-chemistry/pdbmat

Files

• CMakeLists.txt

Manifest