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This section describes the input variables associated with an input_style setting of 'explicit'.
Requires explicit declaration of all terms of the force field that describes this molecule type. This is most difficult way to set up the molecule
information, but it also allows the most flexibility.
This option is only recommended when it is not possible to use the more sophisticated options to set up the molecule of interest.
nunit (integer)
- The number of atoms (or united-atoms) in this molecule. Must be less than or equal to NUMAX
(see preproc.h).
nmaxcbmc (integer)
lpdbnames (logical)
- .TRUE. : to enable the input of 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. : to disable the input of additional pdb information. This does not disable the output of pdb files, it just means thing like
the Rasmol cartoon feature will not work properly.
The variables listed immediately below (unit through improper) are listed as a group for each atom in the molecule.
These are repeated one time 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.
unit (integer), ntype (integer), qqatom (double precision)
- unit 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.
- ntype is the integer used to determine the force field parameters. You will need to look in the towhee_ff_xxx force field
files you are utilizing in order to find the number that you wish to use.
- qqatom is the charge on this atom.
pdbname (character), aminonum (integer), aminoshort (character)
Note: These variables only need to be listed if lpdbnames = .true.
- 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.
- aminonum: The number of each amino acid starting from the N-terminus.
- aminoshort: The three letter code for each amino acid, or other group (such as caps on the C or N termini).
vibration
- invib (integer)
- 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 preproc.h).
- ijvib (integer), itvib (integer)
- The next invib lines underneath the vibration heading are a list of the bond partner and bond force field number for the
invib atoms that are bonded to the current atom. Thus if you have 4 vibrations the next 4 lines will list the bond partner and bond
force field number for each bond.
bending
- inben (integer)
- The first line under the bending heading is the number of bond bending angles that terminate at the current atom. You must list
all bond bending angles which have the current atom at one of the ends, but you do not list bond bending angles which contain
the current atom in the center. Must be a number between 0 and MAXBEND (see preproc.h).
- ijben2 (integer), ijben3(integer), itben (integer), orderben (integer)
- The next inben lines underneath the bending heading are a list of the other atoms in the bond bending angle and the bond bending angle
force field number for the inben angles that contain the current atom at one of the ends. The format for listing the angle is to consider
the current atom in the first position of an angle between atoms current-ijben2-ijben3 so you only need to list atoms ijben2 and ijben3, the
bending type, and the bending order on each line, where there is one angle per line of towhee_input. The bending order is only used for force
fields that have parameters that depend upon the order of the three atoms in the bond - typically those that have class 2 cross terms.
Valid entries for the bending order are
- 1 : the atoms in the bending angle force field are in the same order as the atoms listed here
- -1 : the atoms in the bending angle force field are in the reverse order compared to the atoms listed here
- 0 : null entry to make it easy for those force fields that do not depend upon the bending order
torsion
- intor (integer)
- The first line under the torsion heading is the number of dihedral angles (regular torsions) that terminate at the current atom.
You must list all regular torsion angles which have the current atom at one of the ends, but you do not list regular torsion angles
which contain the current atom in the center. Must be a number between 0 and MAXTOR
(see preproc.h).
- ijtor2 (integer), ijtor3(integer), ijtor4 (integer), ittor (integer)
- The next intor lines underneath the torsion heading are a list of the other atoms in the regular torsion angle and the torsion force
field number for the intor torsions that contain the current atom at one of the ends. The format for listing the regular
torsion angle is to consider the current atom in the first position of a dihedral between atoms current-ijtor2-ijtor3-ijtor4 so you only need
to list atoms ijtor2, ijtor3, and ijtor4 and the torsion type on each line, where there is one regular torsion per line of towhee_input.
angle-angle
- inaa (integer)
- The first line under the angle-angle heading is the number of angle-angle terms which have their shared central atom located
at the current atom. You must list all angle-angle terms which have the current atom at the shared central position, but you do not list
angle-angle terms which contain the current atom at one of the ends. Must be a number between 0 and MAXAA
(see preproc.h).
- ijaa0 (integer), ijaa1(integer), ijaa2 (integer), itaa (integer)
- The next inaa lines underneath the angle-angle heading are a list of the other atoms in the angle-angle term and and the angle-angle
force field number for the inaa angle-angle terms that contain the current atom at the shared central atom. The format for listing the
regular torsion angle is to consider the current atom as the central shared atom in the angle-angle term between the angles ijaa0-current-ijaa1
and ijaa0-current-ijaa2. Each angle-angle term is listed on one line according to the format ijaa0, ijaa1, ijaa2 and itaa (the angle-angle type).
improper torsion
- inimprop (integer)
- 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 MAXIMPROP (see preproc.h).
- ijimprop2 (integer), ijimprop3(integer), ijimprop4 (integer), itimprop (integer)
- The next inimprop 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 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 files. In all cases, the three atoms must be bound
to the current atom.
This is the end of the section that is repeated for each atom for input_style 'explicit'
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