Mol2 - Revision history

Frodo at 00:18, 11 March 2014

2014-03-11T00:18:58Z

← Older revision		Revision as of 00:18, 11 March 2014
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	A 'multimol2' file is simply a bunch of mol2 files for the same ligand but different conformations that have been appended to each other. No other formatting is necessary.		A 'multimol2' file is simply a bunch of mol2 files for the same ligand but different conformations that have been appended to each other. No other formatting is necessary.

	[[Category:~~File formats~~]]		[[Category:Formats]]

Frodo at 04:34, 14 February 2014

2014-02-14T04:34:42Z

← Older revision		Revision as of 04:34, 14 February 2014
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	A 'multimol2' file is simply a bunch of mol2 files for the same ligand but different conformations that have been appended to each other. No other formatting is necessary.		A 'multimol2' file is simply a bunch of mol2 files for the same ligand but different conformations that have been appended to each other. No other formatting is necessary.

			[[Category:File formats]]

Therese: 3 revisions

2012-10-08T20:29:21Z

3 revisions

← Older revision	Revision as of 20:29, 8 October 2012
(No difference)

Rgc: adding presumptions about multimol2 formatting

2009-11-10T01:55:24Z

adding presumptions about multimol2 formatting

← Older revision		Revision as of 01:55, 10 November 2009
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	For extensive details on the MOL2 format, as well as example files, please refer to the Tripos web site documentation (http://www.tripos.com/data/support/mol2.pdf).		For extensive details on the MOL2 format, as well as example files, please refer to the Tripos web site documentation (http://www.tripos.com/data/support/mol2.pdf).

			A 'multimol2' file is simply a bunch of mol2 files for the same ligand but different conformations that have been appended to each other. No other formatting is necessary.

Rgc: removing whitespace from beginning of lines

2009-11-10T01:37:59Z

removing whitespace from beginning of lines

← Older revision		Revision as of 01:37, 10 November 2009
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	4.1. Tripos MOL2 Format		4.1. Tripos MOL2 Format

	This format is used for general molecule input and output of DOCK. Although previous versions of DOCK supported an extended PDB format to store molecule information, the current version now uses MOL2 as the molecule format. This format has the advantage of storing all the necessary information for atom features, position, and connectivity. It is also a standardized format that other modeling programs can read. For more information on how to generate MOL2 files from PDB files, go to the Structure Preparation demo.		This format is used for general molecule input and output of DOCK. Although previous versions of DOCK supported an extended PDB format to store molecule information, the current version now uses MOL2 as the molecule format. This format has the advantage of storing all the necessary information for atom features, position, and connectivity. It is also a standardized format that other modeling programs can read. For more information on how to generate MOL2 files from PDB files, go to the Structure Preparation demo.

	Of the many record types in a MOL2 file, DOCK recognizes the following: MOLECULE, ATOM, BOND, SUBSTRUCTURE and SET. In the MOLECULE record, DOCK utilizes information about the molecule name and number of atoms, bonds, substructures and sets. In the ATOM record DOCK utilizes information about the atom names, types, coordinates, and partial charges. In the BOND record, DOCK utilizes the atom identifiers for the bond. In the SUBSTRUCTURE record, DOCK records the fields, but does not utilize them. The SET records are entirely optional. They are used only in special circumstances, like when ligand flexibility is considered. In DOCK 6, an additional record type has been introduced. This is the SOLVATION record, that has the atomic desolvation information for the ligand atoms. The parameter read_mol_solvation can be used to read in this record.		Of the many record types in a MOL2 file, DOCK recognizes the following: MOLECULE, ATOM, BOND, SUBSTRUCTURE and SET. In the MOLECULE record, DOCK utilizes information about the molecule name and number of atoms, bonds, substructures and sets. In the ATOM record DOCK utilizes information about the atom names, types, coordinates, and partial charges. In the BOND record, DOCK utilizes the atom identifiers for the bond. In the SUBSTRUCTURE record, DOCK records the fields, but does not utilize them. The SET records are entirely optional. They are used only in special circumstances, like when ligand flexibility is considered. In DOCK 6, an additional record type has been introduced. This is the SOLVATION record, that has the atomic desolvation information for the ligand atoms. The parameter read_mol_solvation can be used to read in this record.

	For extensive details on the MOL2 format, as well as example files, please refer to the Tripos web site documentation (http://www.tripos.com/data/support/mol2.pdf).		For extensive details on the MOL2 format, as well as example files, please refer to the Tripos web site documentation (http://www.tripos.com/data/support/mol2.pdf).

JohnIrwin at 23:08, 19 September 2006

2006-09-19T23:08:38Z

New page

4.1. Tripos MOL2 Format

This format is used for general molecule input and output of DOCK. Although previous versions of DOCK supported an extended PDB format to store molecule information, the current version now uses MOL2 as the molecule format. This format has the advantage of storing all the necessary information for atom features, position, and connectivity. It is also a standardized format that other modeling programs can read. For more information on how to generate MOL2 files from PDB files, go to the Structure Preparation demo.

Of the many record types in a MOL2 file, DOCK recognizes the following: MOLECULE, ATOM, BOND, SUBSTRUCTURE and SET. In the MOLECULE record, DOCK utilizes information about the molecule name and number of atoms, bonds, substructures and sets. In the ATOM record DOCK utilizes information about the atom names, types, coordinates, and partial charges. In the BOND record, DOCK utilizes the atom identifiers for the bond. In the SUBSTRUCTURE record, DOCK records the fields, but does not utilize them. The SET records are entirely optional. They are used only in special circumstances, like when ligand flexibility is considered. In DOCK 6, an additional record type has been introduced. This is the SOLVATION record, that has the atomic desolvation information for the ligand atoms. The parameter read_mol_solvation can be used to read in this record.

For extensive details on the MOL2 format, as well as example files, please refer to the Tripos web site documentation (http://www.tripos.com/data/support/mol2.pdf).