Dr. Jason L. Sonnenberg > Chemistry-ESPT > Chemistry::ESPT::Aprmtop

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Module Version: 0.03   Source  

NAME ^

Chemistry::ESPT::Aprmtop - AMBER prmtop file object.

SYNOPSIS ^

    use Chemistry::ESPT::Aprmtop;

    my $prmtop = Chemistry::ESPT::Aprmtop->new();

DESCRIPTION ^

This module provides methods to quickly access data contained in an AMBER prmtop file. AMBER prmtop files can only be read currently.

ATTRIBUTES ^

All attributes are currently read-only and get populated by reading the assigned ESS file. Attribute values are accessible through the $Aprmtop->get() method.

CHARGE

Total molecular charge given by (total number of protons) - (total Molecular Mechanics charge). Values rounded to nearest integer.

MMCHARGE

Molecular mechanic atomic charges as determined by AMBER stored as an NATOM array.

METHODS ^

Method parameters denoted in [] are optional.

$prmtop->new()

Creates a new Aprmtop object

$prmtop->analyze(filename [spin])

Analyze the spin results in file called filename. Spin defaults to Alpha.

NOTES ^

Aprmtop uses the atomic masses found in the prmtop file to determine atomic symbols. For elements possessing the same integer atomic mass, such as Ar and Ca, Aprmtop relies on the atom name section of the prmtop file. If those atom names are not atomic symbols followed by an optional integer and separated by a space(s), then the resulting values in ATOMS may not be correct.

VERSION ^

0.03

SEE ALSO ^

Chemistry::ESPT::ESSfile, http://amber.scripps.edu

AUTHOR ^

Dr. Jason L. Sonnenberg, <sonnenberg.11@osu.edu>

COPYRIGHT AND LICENSE ^

Copyright 2008 by Dr. Jason L. Sonnenberg

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. I would like to hear of any suggestions for improvement.

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