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<title>MCCCS Towhee (input_style 'basic connectivity map')</title>
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</a>MCCCS Towhee (input_style 'basic connectivity map')</font></b></font>
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This section describes the input variables associated with an <b>input_style</b> setting of 'basic connectivity map'.
Atom-based connectivity map, with the details of the force
field parameters determined via the buildmolec and assemble routines. This documentation is only maintained for the current version of the code and was
last modified for Version 5.1.0. This molecule assembly option was the standard way to set up any molecule that is not supported by one of the
polymer builder options. It is still available as an option, although the <a href="inpstyle_6.html">advanced connectivity map</a> option is suggested
for most users as it provides a powerful and flexible version of this builder.
The 'basic connectivity map' option requires the specification of a forcefield and the appropriate parameter names for that force field. The individual
web pages for each of the force fields (summarized on the <a href="../towhee_capabilities.html">Towhee Capabilities</a> page for more information about
the atom names. This feature enables the automatic determination of all of the vibration types, bending angles, bending types, regular torsion angles,
regular torsion types, angle-angle terms, angle-angle types, and improper torsion types that are implied by the bonding structure of the molecule.
The automatic atom assignment for the improper torsions is not possible with this option and users who require that feature should use the
<a href="inpstyle_6.html">advanced connectivity map</a> option.
<p> </p>
<dt><a name="nunit"><b>nunit (integer)</b></a>
<ul>
<li> The number of atoms (or united-atoms) in this molecule. Must be less than or equal to NUMAX
(see <a href="../code/code_manual.html#preproc">preproc.h</a>).
</li>
</ul>
</dt>
<dt><a name="nmaxcbmc"><b>nmaxcbmc (integer)</b></a>
<ul>
<li> The maximum number of atoms to regrow during a <a href="../code/cbmc.html">configurational-bias</a> regrowth move.
It is normally best to set this to the same value as <b>nunit</b>, but if a user observes that no configurational-bias regrowth moves beyond
a certain size are ever accepted then it is more efficient to set <b>nmaxcmbc</b> to the largest value where moves are accepted to avoid
wasting effort on move that are so likely to fail.
</li>
</ul>
</dt>
<dt><a name="lpdbnames"><b>lpdbnames (logical)</b></a>
<ul>
<li>.TRUE. if you want to input information about the pdb (protein data bank) atom name, amino acid number, amino acid name. This
information is needed in order to use the cartoon feature of certain pdb viewers (such as <a href="../software.html#rasmol">Rasmol</a>).
</li>
<li>.FALSE. if you don't need that feature. This does not disable the output of a pdb file, it just means things like the cartoon feature will
not work properly in <a href="../software.html#rasmol">Rasmol</a>.
</li>
</ul>
</dt>
<dt><a name="forcefield"><b>forcefield (character*10)</b></a>
<ul>
<li>The forcefield that you want to use to build this molecule. A summary of available force fields is provided on the
<a href="../towhee_capabilities.html">Towhee Capabilities</a> page.
</li>
</ul>
</dt>
<dt><a name="charge_assignment"><b>charge_assignment (character*30)</b></a>
<ul>
<li>'bond increment': the bond increment method is used to assign the charges on each atom and the variable <b>qqatom</b> is not required.
Note that this method is only functional for certain forcefields. Please check the individual force field documentation to see if this is
available for your force field of interest.
</li>
<li>'manual': the charges on each atom are manually specified in the towhee_input file as the variable <b>qqatom</b> in the following section.</li>
<li>'none': a zero charge is assigned to each atom and the variable <b>qqatom</b> is not required.</li>
</ul>
</dt>
<p> </p>
<font color="red"> The variables listed immediately below (unit through improper) are listed as a group for each atom in the molecule. Thus, you
input all of the information about the first atom before you list information for the subsequent atoms.
</font>
<dt><a name="unit"><b>unit (integer), type (character), qqatom (double precision)</b></a>
<ul>
<li><b>unit</b> is the number of the atom in order starting from atom number 1. This is only used to help the user keep track of the
molecule as they are building it in the input file. If the unit number listed in towhee_input does not match the running total
of unit numbers in Towhee then the code will stop with an error message.
</li>
<li><b>ntype</b> is the character string that contains the atom type for the forcefield. Information about valid atomtypes is found
in the documentation for each force field (summarized on the <a href="../towhee_capabilities.html">Towhee Capabilities</a> page).
</li>
<li><b>qqatom</b> is the charge on this atom. This is only required if the <b>charge_assignment</b> variable is set to 'manual'.</li>
</ul>
</dt>
<dt><a name="pdbname"><b>pdbname (character), aminonum (integer), aminoshort (character)</b></a>
<dt>Note: These variables only need to be listed if lpdbnames = .true.</dt>
<ul>
<li> pdbname: A four letter/number string that is output in the pdb file. The precise spacing is important if you want to get most pdb
viewers to recognize the atoms as the pdb file is extremely specific.
</li>
<li> aminonum: The number of each amino acid starting from the N-terminus.</li>
<li> aminoshort: The three letter code for each amino acid, or other group (such as caps on the C or N termini).</li>
</ul>
</dt>
<dt><b>vibration</b>
<ul>
<dt><a name="invib"><b>invib (integer)</b></a>
<ul>
<li> The first line under the vibration heading is the number of atoms that are bonded to the current atom. Must be a number between
0 and NNBOND (see <a href="../code/code_manual.html#preproc">preproc.h</a>).
</li>
</ul>
</dt>
<dt><a name="ijvib"><b>ijvib (integer)</b></a>
<ul>
<li> The second line contains the atom numbers for all <b>invib</b> atoms that are bonded to the current atom. </li>
</ul>
</dt>
</ul>
</dt>
<dt><b>improper torsion</b>
<ul>
<dt><a name="inimp"><b>inimprop (integer)</b></a>
<ul>
<li> The first line under the improper heading is the number of improper torsions (any form) which have the central atom located at the current
atom. You must list all improper torsions which have the current atom at the central position, but you do not list improper torsions which contain
the current atom at one of the ends. Must be a number between 0 and <b>MAXIMPROP</b> (see <a href="../code/code_manual.html#preproc">preproc.h</a>).
</li>
</ul>
</dt>
<dt><a name="ijimprop2"><b>ijimprop2 (integer), ijimprop3(integer), ijimprop4 (integer), itimprop (integer)</b></a>
<ul>
<li> The next <b>inimprop</b> lines underneath the improper torsion heading are a list of the other atoms in the improper torsion and the improper
force field number for the <b>inimprop</b> improper torsions that contain the current atom at the central atom. There are currently three different
forms of improper torsions, and these forms are specified in the force field. In all cases, the three atoms must all be bound to the current atom.
If you want the program to determine the improper torsion type then just enter an itimprop value of 0.
</li>
</ul>
</dt>
</ul>
</dt>
<dt><font color="red"> This is the end of the section that is repeated for each atom for input_style 'basic connectivity map'</font></dt>
<hr></hr>
<a href="../index.html">Return to the main towhee web page</a>
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<i><font size="2">Send comments to:</font></i>
<font size="2"> <a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a>
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<i>Last updated:</i> <!-- #BeginDate format:Am1 -->February 09, 2010<!-- #EndDate -->
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