MM_SYSTEM


Function

MM_System contains a procedure for constructing an MM system definition from data read in from an MM file and a sequence file. Essentially MM_System fills the variables in the module MM_TERMS.

Full details about the use of this module and the format of a sequence file can be found in chapter 5 of the book A Practical Introduction to the Simulation of Molecular Systems.

Dependencies

Module Variables
DEFINITIONS DP, MAX_RECORD_LENGTH
ELEMENTS MASS
FILES NEXT_UNIT
IO_UNITS INPUT, OUTPUT
PARSING Most public items in the module.
STATUS ERROR
ATOMS Most public items in the module.
CONNECTIVITY Most public items in the module.
MM_FILE_DATA Most public items in the module.
MM_FILE_IO MM_FILE_READ
MM_TERMS Most public items in the module.
SEQUENCE Most public items in the module.
SYMMETRY Most public items in the module.


Public Variables

None.

Public Procedures

There is a single public subroutine in this module.

SubroutinePurpose
MM_SYSTEM_CONSTRUCT Define the terms necessary to calculate the MM energy for a system.


MM_SYSTEM_CONSTRUCT

Argument Type Intent Optional Purpose
MMFILE Character ( Len = * ) In No The name of a processed binary MM file.
SEQUENCE Character ( Len = * ) In Yes The name of the sequence file.


Error Place Meaning
I/O Error. MM_SYSTEM_CONSTRUCT There is a problem opening the scratch file needed by the subroutine.
Missing energy function parameters. FILL_ATOMS_AND_MM_TERMS Some MM term parameters were not defined.
The last residue cannot have a `+R' bond specification. GENERATE_STRUCTURE The last residue in a system cannot be joined to a following residue except by using a variant.
Unknown atom name: XXX. GENERATE_STRUCTURE An atom in a bond or improper definition is unknown.
A bond contains no non-link atoms. GENERATE_STRUCTURE A bond specification has only `+R' or `-R' atoms.
Only one connection to the previous residue is allowed. GENERATE_STRUCTURE There can only be one bond specified to the preceding residue using the `-R' syntax.
Invalid bond to a previous residue. GENERATE_STRUCTURE The previous residue did not have a bond specified with a `+R' atom.
Only one connection to the next residue is allowed. GENERATE_STRUCTURE There can only be one bond specified to the following residue using the `+R' syntax.
Invalid bond atom index. GENERATE_STRUCTURE There has been a problem constructing the bond lists for a residue.
Improper specified to previous residue without bond to `-R'. GENERATE_STRUCTURE A `-R' atom was given in an improper definition but without the corresponding bond specification.
Improper specified without corresponding `+R' bond. GENERATE_STRUCTURE A `+R' atom was given in an improper definition but without the corresponding bond specification.
There is a missing `*R' specification in a link. GENERATE_STRUCTURE A cross-linking bond specification is missing from a LINK statement.
Unknown atom to delete: XXX. GENERATE_STRUCTURE Cannot find the atom which is to be deleted when applying a link or variant modification to a residue.
Unknown atom to change charge: XXX. GENERATE_STRUCTURE Cannot find the atom whose charge to change when applying a link or variant modification to a residue.
I/O Error. READ_SEQUENCE_FILE There is a problem with the sequence file.
SEQUENCE label invalid. READ_SEQUENCE_FILE The `Sequence' tag is missing from the top of the sequence file.
SUBSYSTEM label invalid. READ_SEQUENCE_FILE A `Subsystem' tag is missing.
Duplicate subsystem names. READ_SEQUENCE_FILE Two subsystems have the same name.
Subsystem residue count error. READ_SEQUENCE_FILE The number of residues specified for a subsystem and listed for its sequence are different.
Unknown residue name: XXX. READ_SEQUENCE_FILE A residue name specified in a subsystem sequence definition could not be found in the MM file data.
Invalid residue name or number in VARIANT statement. READ_SEQUENCE_FILE A residue specified in a VARIANT statement could not be found in the sequence.
Unknown variant name: XXX. READ_SEQUENCE_FILE A variant name specified in a VARIANT statement could not be found in the MM file data.
Invalid subsystem block terminator. READ_SEQUENCE_FILE An 'End' tag was missing at the end of a subsystem definition block.
Unknown link name: XXX. READ_SEQUENCE_FILE A link name specified in a LINK statment could not be found in the MM file data.
Unknown link subsystem name: XXX. READ_SEQUENCE_FILE A subsystem name specified in a LINK statement could not be found in the sequence.
Invalid residue name or number in LINK statement. READ_SEQUENCE_FILE A residue specified in a LINK statement could not be found in the sequence.
Invalid sequence block terminator. READ_SEQUENCE_FILE An `End' tag was missing at the end of the sequence file.




Stability

Stable.



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