/usr/share/gromacs/top/residues.dtd is in gromacs-data 2016.1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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<!-- GROMACS Data type description (DTD).
This source code is part of
G R O M A C S
GROningen MAchine for Chemical Simulations
VERSION 3.1
Copyright (c) 1991-2002
BIOSON Research Institute, Dept. of Biophysical Chemistry
University of Groningen, The Netherlands
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
If you want to redistribute modifications, please consider that
scientific software is very special. Version control is crucial -
bugs must be traceable. We will be happy to consider code for
inclusion in the official distribution, but derived work must not
be called official GROMACS. Details are found in the README & COPYING
files - if they are missing, get the official version at www.gromacs.org.
To help us fund GROMACS development, we humbly ask that you cite
the papers on the package - you can find them in the top README file.
Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
And Hey:
GROningen Mixture of Alchemy and Childrens' Stories
David van der Spoel 07/2001, 03/2002
The authorative version of this document can be found at
http://www.gromacs.org/gromacs3.1.dtd
and also in the library directory of your local GROMACS
installation.
Please use the following formal public identifier to identify it:
"-//RESIDUES//DTD Residues XML V1.0//EN"
<!DOCTYPE residues PUBLIC "-//RESIDUES//DTD Gromacs XML V3.1.0//EN"
"http://www.gromacs.org/residues.dtd"
[...]>
-->
<!-- This file defines the structure of the information necessary make
a molecule from simple building blocks (called residues). The
algorithm processing a sequence (or pdb file) should follow these
steps:
1. Do all the modification (moddef)
2. Add all the links between residues
3. Generate hydrogens
4. Generate angle and torsion descriptions
-->
<!ELEMENT macromolecules (residues,macromolecule*)>
<!ELEMENT residues (residue*,linkdef*,moddef*)>
<!ELEMENT residue (ratom+,rbond*,rangle*,rimproper*,rdihedral*,raddh*)>
<!ATTLIST residue
restype ID #REQUIRED
longname CDATA #REQUIRED>
<!-- We can not use ID here for atom names since there is no -->
<!-- hope to make them unique, e.g. all amino acids have the -->
<!-- same name for backbone atoms. -->
<!ELEMENT ratom EMPTY>
<!ATTLIST ratom
name CDATA #REQUIRED>
<!ELEMENT rbond EMPTY>
<!ATTLIST rbond
a1 CDATA #REQUIRED
a2 CDATA #REQUIRED>
<!ELEMENT rangle EMPTY>
<!ATTLIST rangle
a1 CDATA #REQUIRED
a2 CDATA #REQUIRED
a3 CDATA #REQUIRED>
<!ELEMENT rimproper EMPTY>
<!ATTLIST rimproper
a1 CDATA #REQUIRED
a2 CDATA #REQUIRED
a3 CDATA #REQUIRED
a4 CDATA #REQUIRED>
<!ELEMENT rdihedral EMPTY>
<!ATTLIST rdihedral
a1 CDATA #REQUIRED
a2 CDATA #REQUIRED
a3 CDATA #REQUIRED
a4 CDATA #REQUIRED>
<!-- Definition of how to add (hydrogen) atoms to molecules -->
<!-- using a certain geometry (see GROMACS manual) -->
<!ELEMENT raddh EMPTY>
<!ATTLIST raddh
hclass ( polar | aromatic | aliphatic )
addgeom CDATA #REQUIRED
addnum CDATA #REQUIRED
addto CDATA #REQUIRED>
<!-- Define a covalent link between two residues, given in restyp -->
<!-- and the atoms are given as well (atomprev and atomnext) -->
<!-- A reference distance between the atoms does also have to be -->
<!-- given in nm (but that does not have to be used). -->
<!ELEMENT linkdef EMPTY>
<!ATTLIST linkdef
linktype ID #REQUIRED
restype IDREFS #REQUIRED
atomprev CDATA #REQUIRED
atomnext CDATA #REQUIRED
refdist CDATA #REQUIRED>
<!-- Description of termini, etc. or maybe other modifications too -->
<!-- It is important that the implementation deletes first, and -->
<!-- adds atoms afterwards -->
<!ELEMENT moddef (moddelete*,modadd*,modrepl*)>
<!ATTLIST moddef
modtype ID #REQUIRED>
<!ELEMENT moddelete EMPTY>
<!ATTLIST moddelete
delname CDATA #REQUIRED>
<!ELEMENT modreplace EMPTY>
<!ATTLIST modreplace
oldname CDATA #REQUIRED
newname CDATA #REQUIRED>
<!ELEMENT modadd EMPTY>
<!ATTLIST modadd
addname CDATA #REQUIRED
addbond CDATA #REQUIRED>
<!-- Generic stuff to define proteins etc. as built up from blocks -->
<!-- such as amino acids and HEME etc. -->
<!ELEMENT macromolecule (mblock+,mlink*,mmod*)>
<!ATTLIST macromolecule
mname ID #REQUIRED>
<!ELEMENT mblock EMPTY>
<!ATTLIST mblock
resname ID #REQUIRED
restype IDREF #REQUIRED
protonated ( no | polar | all ) "polar">
<!ELEMENT mlink EMPTY>
<!ATTLIST mlink
mlinktype ( peptide | disulphide | special ) "peptide"
resname IDREFS #REQUIRED>
<!ELEMENT mmod EMPTY>
<!ATTLIST mmod
resname IDREF #REQUIRED
modtype IDREF #REQUIRED>
<!-- Generic stuff to define proteins etc. as built up from blocks -->
<!-- such as amino acids and HEME etc. -->
<!ELEMENT macromolecule (mblock+,mlink*,mmod*)>
<!ATTLIST macromolecule
mname ID #REQUIRED>
<!ELEMENT mblock EMPTY>
<!ATTLIST mblock
resname ID #REQUIRED
restype IDREF #REQUIRED
protonated ( no | polar | all ) "polar">
<!ELEMENT mlink EMPTY>
<!ATTLIST mlink
mlinktype ( peptide | disulphide | special ) "peptide"
resname IDREFS #REQUIRED>
<!ELEMENT mmod EMPTY>
<!ATTLIST mmod
resname IDREF #REQUIRED
modtype IDREF #REQUIRED>
|