-
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.
.TRUE.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.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 parameters 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.
-
The atom number starting from 1, the number code for the nonbonded force field, and the charge on this atom.
.TRUE.
-
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. Then the number of each amino acid starting from the N-terminus.
Finally, a the three letter code for each amino acid, or other group (such as caps on the C or N termini). All on a single line.
- The first line under the vibration heading is the number of atoms that are bonded to the current atom (internally stored as invib). Must be between 0 and NNBOND.
- 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.
- The first line under the bending heading is the number of bond bending angles that terminate at the current atom (internally stored as inben). You must list all bond bending angles that have the current atom at one of the ends, but you do not list bond bending angles that contain the current atom in the center. Must be a number between 0 and MAXBEND.
- The next inben lines underneath the bending heading are a list of the other atoms in the bond bending angle
(internally ijben2 and ijben3),
the integer type of the bending angle (internally itben),
the order of the bending angle that is used for force fields with assymetric bending angles (internally orderben),
the bond-angle type (internally itbang),
and the order of the bond-angletype (internally orderbang).
The bending angle order and bond-angle order are 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 orderben and orderbang order are as follows.
- 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 for force fields that do not depend upon the bending order
- The first line under the torsion heading is the number of regular torsions that terminate at the current atom (internaly intor). 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 that contain the current atom in the center positions. Must be a number between 0 and MAXTOR.
- The next intor lines underneath the torsion heading are a list of the other atoms in the regular torsion angle (internally ijtor2, ijtor3, ijtor4), and the torsion force field number (internally ittor) for the intor torsions that contain the current atom at one of the ends.
- 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 (internally inaa). 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 that contain the current atom at one of the ends. Must be a number between 0 and MAXAA.
- The next inaa lines underneath the angle-angle heading are a list of the other atoms in the angle-angle term (internally ijaa0, ijaa1, ijaa2), and and the angle-angle force field number (internally itaa) for the inaa angle-angle terms that contain the current atom at the shared central atom. The format for listing the angle-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.
- The first line under the improper heading is the number of improper torsions (any form) that have the central atom located at the current atom (internally inimprop). You must list all improper torsions that 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 files. In all cases, the three atoms must be bonded to the current atom.
This is the end of the section that is repeated for each atom for input_style 'explicit'