buildmolec.F and
assemble.F subroutines.
This documentation is maintained for the current version of the code and was
last modified for Version 8.0.0. The 'advanced connectivity map' option is a more 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.
See the individual manual pages for each force field (summarized on Towhee Capabilities) for detailed 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.
However, automatic determination of atoms that require an improper torsion is not possible with this option and users who require that feature should use the
'advanced connectivity map' option.
-
The number of atoms (or united-atoms) in this molecule. Must be less than or equal to NUMAX.
-
The maximum number of atoms to regrow during a configurational-bias regrowth move.
It is safe to set this to the value of nunit, but no configurational-bias regrowth moves beyond
a certain size are ever accepted then it is more efficient to set this to the largest value where moves are accepted to avoid
wasting effort on move that are very likely to fail.
.TRUE.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 Rasmol)..FALSE.do not input additional pdb information. This does not disable the output of a pdb file, it just means things like the protein cartoon feature might not work properly in Rasmol.
-
The forcefield that you want to use to build this molecule. A summary of available force fields is provided on the
Towhee Capabilities page.
- 'bond increment': the bond increment method is used to assign the charges on each atom and the parameter charge 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.
- 'manual': the charges on each atom are manually specified in the towhee_input file as the parameter charge in the following section.
- 'none': a zero charge is assigned to each atom and the parameter charge is not required.
This section is repeated for each atom in the molecule.
-
Three parameters listed on a single line.
First, unit is the number of the atom in order starting from atom number 1. This is 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.
Second, atomname 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 Towhee Capabilities page).
Finally, charge is the charge on this atom.
This is only required if the charge_assignment is set to 'manual'.
.TRUE.
-
Three parameters on a single line.
First, 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.
Second, the number of each amino acid starting from the N-terminus.
Third, the three letter code for each amino acid, or other group (such as caps on the C or N termini).
- The first line under the vibration heading is the number of atoms that are bonded to the current atom (internally invib). Must range from 0 to NNBOND.
- The second line contains the atom numbers for all invib atoms that are bonded to the current atom.
- 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 (internally inimprop. 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 MAXIMPROP.
- The next inimprop lines underneath the improper torsion heading are a list of the other atoms in the improper torsion (internally ijimprop2, ijimprop3, ijimprop4) and the improper force field number (internally itimprop) for the inimprop 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 Towhee to automatically determine the improper torsion type then enter an itimprop value of 0.
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