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This appendix contains a description of the various topology files available for CONGEN users. For CONGEN version 2 and beyond, we anticipate providing only one topology file in binary form, but all older and obsolete files will be provided in source form, although they may not be readable without some editing. All topology files are stored in `CGDATA'. The file names used consists of an alphabetic part followed by a number, e.g. RTOPH. There are two copies of each file; one with extension, `.INP', which is a character files used as an command file to generate the binary file, with extension, `.MOD'. The `.INP' is meant for human eyes; the `.MOD' files are meant for CONGEN to read. The numeric part of each name is its version number. In general, one should use the highest version number of a file.
Five types of residue topology files are currently available. Three contain the twenty amino acids, but with different representations. `RTOPn' holds extended atom topologies; `RTOPHn' holds explicit hydrogen residue topologies; and `RTOPALLHn' holds all hydrogen residue topologies. The fourth topology file type, `RTOPDNAn', is for DNA residues and the phosphates connecting them. These DNA files have not been used very much, so results obtained using them must be treated with especial care. Also, the DNA and protein files cannot be used together because of differences in the selection of atom type codes.
The fifth type of topology file is the AMBER topology file based on the AMBER potential(37). At the present time, only the united atom topology file is available.
The remainder of this section lists the comments in the topology file themselves, along with some further explanations of the rationale behind particular versions.
Explicit hydrogen topology files
All hydrogen topology files
DNA topology files
AMBER topology files
`RTOP8' is a modification of `RTOP7' that has all the atoms specified in PARAM5. In addition, all atoms are typed as hydrogen bond donors and acceptor for use by the GENERATE command in the RTF reader, see section The Format of a Residue Topology File. The linkages between residues are corrected as required in Congen v.2, and D amino acids are added.
Title in the topology file:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 8 * CONVERTED TO NEW FORMAT -- 10/29/81 * HBOND 2nd donor antecdants CA for peptides CD for arg he 30-Dec-1981 * PCA and PC added by Robert Bruccoleri, 2/20/91 * Adapted for symbolic generation, Congen v2, REB 30-Jul-1991. * D amino acids added, REB 9-Sep-1991.
`RTOP7' is `RTOP6' converted to free field input format.
Title in the run:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 7 * CONVERTED TO NEW FORMAT 10/29/81 -- BRB * HBOND 2nd antecedants converted to CA for peptides and CD arg he
Title in the topology file:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 7 * CONVERTED TO NEW FORMAT -- 10/29/81 * HBOND 2nd donor antecdants CA for peptides CD for arg he 30-Dec-1981
New set of atom names for the bilder information was added by Bernie. Values for setting the position of the CB carbons added.
Comments taken from the run itself:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 5 * DEFINED WITH 19 ATOM TYPES -- RESIDUES FOR AMINO ACIDS, HEME AND * WATER -- INCLUDES IMPROPER TORSIONS -- COMPILED BY WVG, BDO AND * SNS -- 3/15/79 * PROTEIN BUILDER INFORMATION ADDED 11/24/79 -- BDO
Title actually in the file:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 3 * DEFINED WITH 19 ATOM TYPES -- RESIDUES FOR AMINO ACIDS, HEME AND * WATER -- INCLUDES IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENT ARRAYS * COMPILED BY WVG, BDO AND SNS -- 3/15/79 * LAST UPDATE -- 9/3/79 -- BRB
Comments taken from the file itself:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 5 * DEFINED WITH 19 ATOM TYPES -- RESIDUES FOR AMINO ACIDS, HEME AND * WATER -- INCLUDES IMPROPER TORSIONS -- COMPILED BY WVG, BDO AND * SNS -- 3/15/79 * PROTEIN BUILDER INFORMATION ADDED 11/24/79 -- BDO
The title in the binary file:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 3 * DEFINED WITH 19 ATOM TYPES -- RESIDUES FOR AMINO ACIDS, HEME AND * WATER -- INCLUDES IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENT ARRAYS * COMPILED BY WVG, BDO AND SNS -- 3/15/79 * LAST UPDATE -- 4/3/79 -- BDO AND SNS
Note: the bilder information referred to above is the atoms involved for each internal coordinate. The five real numbers required are blank.
Comments taken from file itself:
* RESIDUE TOPOLOGY FILE FOR EXTENDED ATOMS -- VERSION 3 * DEFINED WITH 19 ATOM TYPES -- RESIDUES FOR AMINO ACIDS, HEME AND * WATER -- INCLUDES IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENT ARRAYS * COMPILED BY WVG, BDO AND SNS -- 3/15/79 * LAST UPDATE -- 4/3/79 -- BDO AND SNS
Comments taken from the file itself:
* RESIDUE TOPOLOGY FILE USING EXTENDED ATOMS -- VERSION 1 * BRG TOPOLOGY FILE FOR PTI IS A SUBSET OF THIS FILE -- NO IMPROPER * TORSIONS ARE INCLUDED -- LAST UPDATE 4/10/79 -- BDO AND SNS
`RTOPH8' is basically `RTOPH7' converted for symbolic generation. D amino acids are also included. Title in run:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 7 -- BRB -- 10/24/81 * DEVELOPMENTAL VERSION FOR CHARMM_16 * RESIDUE 'FRM' AND 'ACE' DELETED - BRB 10/24/81 * BUILDER INFORMATION GIVEN FOR ALL EXPLICIT HYDROGENS - BRB 10/24/81 * CONVERTED TO NEW FORMAT - BRB 10/26/81 * H bond second antecedants changed to fix ARG and cis peptides DJS 12/26/81
Title in file:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 7 -- BRB -- 10/20/81 * BUILDER INFORMATION CORRECT TO DETERMINE ALL EXPLICIT HYDROGENS * H bond second antecdants set to CA for peptides and CD for ARG NE
`RTOPH7' is basically `RTOPH6' converted to free field input.
Title in run:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 7 -- BRB -- 10/24/81 * DEVELOPMENTAL VERSION FOR CHARMM_16 * RESIDUE 'FRM' AND 'ACE' DELETED - BRB 10/24/81 * BUILDER INFORMATION GIVEN FOR ALL EXPLICIT HYDROGENS - BRB 10/24/81 * CONVERTED TO NEW FORMAT - BRB 10/26/81 * H bond second antecedants changed to fix ARG and cis peptides DJS 12/26/81
Title in file:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 7 -- BRB -- 10/20/81 * BUILDER INFORMATION CORRECT TO DETERMINE ALL EXPLICIT HYDROGENS * H bond second antecdants set to CA for peptides and CD for ARG NE
The changes that have been made to date are the inclusion of two additional improper dihedrals spanning the rings of tryptophan to distribute the out of plane bending forces more evenly. When used with the `PARAM1' parameters, see section Development of the PARAM1 Parameter Set, this gives a correct out of plane skeletal vibration for tryptophan at between 400 and 500 cm-1 with relatively few high frequency modes induced by coupling of improper dihedral terms.
A second change is the repair of an error in the angles of the heme residue. Two angles were transposed in the second and third atoms resulting in incorrect specification of the desired angle. The old angles were 6-9-10 and 3-9-10. The correct angles are 6-10-9 and 3-10-9. This change results in a lower angle energy for the heme, but little change in geometry.
A third set of changes have been made in the builder information sections of the aromatic rings. The dihedral angle values have been set so that more or less correct rings will be built (the old values would result in figure eights and other such oddities).
Title in the topology file itself:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 5 -- BRB -- 9/3/80 * BILDER INFORMATION INCLUDED FOR ALL ATOMS
Numbers for all the bilder values are present. No difference in other information with `RTOPH5' or `RTOPH4'.
Title in the topology file itself:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 4 -- SNS AND BDO -- 1/24/80 * BILDER INFORMATION ADDED - WATER CHARGES CHANGED * IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENTS ADDED
This file differs from `RTOPH4' in that backbone atoms needed for building have been added. No numbers are specified.
Title in the topology file itself:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 4 -- SNS AND BDO -- 1/24/80 * BILDER INFORMATION ADDED - WATER CHARGES CHANGED * IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENTS ADDED
The BILDER information added is just blank lines so that the RTF reading routine reads the right number of records.
Title in the topology file itself:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN * ATOMS -- VERSION 2 -- SNS AND BDO -- 4/4/79 * IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENTS ADDED
This file is a modification of `RTOPALLH6' where all of the bilder records have been inserted and checked. This file was modified for symbolic generation and to include D-amino acids. Earlier Bugs were corrected. These modifications were made by Donna Bassolino and Bob Bruccoleri.
Run title:
* rtf creation run for allh * ! ! The charges in this file were set up using the experimental formamide ! and N-methyl acetamide dipole moments of 3.7 D through the following ! procedure. ! 1 - the C=O and N-H2 of formamide were required to be neutral ! 2 - the HA charge was arbitrarily set to zero (various Mulliken ! population analyses give it small magnitude and variable ! sign). ! 3 - The above conditions and the direction of the formamide dipole ! competely determine the formamide charges ! 4 - The CA peptide charge was arbitrarily set to 0.1 (various ! Mulliken population analysis give it 0.0 to 0.12 charges). ! 5 - The peptide charges were obtained by keeping the same C=O ! and HN charges. This requires a readjustment of the ! N charge to maintain neutrality. ! ! The resulting set of charges gives close to the same dipole moment ! when applied to N-methyl acetamide, but a somewhat different ! direction. ! read rtf card * Residue Topology File for Proteins Using All Atom Hydrogens (ALLH) * Cambridge notation for atom names * atom type 3 ha added for aliphatic hydrogens * atom type 16 ct added for tetrahedral carbons * Impropers rearranged to match rtoph7 for gaunido & sidechain amide n * 2nd donor antecedants converted to CA for peptides CD for arg HE * Amide charges from Hayes and Kollman JACS 98:3335,7811 (1796) * HA charges from Wiberg and Wendoloski J. Comp. Chem. 2:53 (1981) * IC's added, and file checked, Donna Bassolino, March 1990 * Adapted for symbolic generation, Robert Bruccoleri, July 1991
Title in the file:
* Residue Topology File for Proteins Using All Atom Hydrogens (ALLH) * Cambridge notation for atom names * 2nd donor antecedants converted to CA for peptides CD for arg HE * Amide charges from Hayes and Kollman JACS 98:7811 (1796) * HA charges from Wiberg and Wendoloski J. Comp. Chem. 2:53 (1981) * IC's added, and file checked, Donna Bassolino, March 1990 * Adapted for symbolic generation, Robert Bruccoleri, July 1991 * Redundent IC's removed for methyl groups Donna Bassolino Aug 1991
This file is a modification of `RTOPALLH5' where all of the bilder records have been inserted and checked. These modifications were made by Donna Bassolino.
Run title:
* rtf creation run for allh * ! ! The charges in this file were set up using the experimental formamide ! and N-methyl acetamide dipole moments of 3.7 D through the following ! procedure. ! 1 - the C=O and N-H2 of formamide were required to be neutral ! 2 - the HA charge was arbitrarily set to zero (various Mulliken ! population analyses give it small magnitude and variable ! sign). ! 3 - The above conditions and the direction of the formamide dipole ! competely determine the formamide charges ! 4 - The CA peptide charge was arbitrarily set to 0.1 (various ! Mulliken population analysis give it 0.0 to 0.12 charges). ! 5 - The peptide charges were obtained by keeping the same C=O ! and HN charges. This requires a readjustment of the ! N charge to maintain neutrality. ! ! The resulting set of charges gives close to the same dipole moment ! when applied to N-methyl acetamide, but a somewhat different ! direction. ! read rtf card * Residue Topology File for Proteins Using All Atom Hydrogens (ALLH) * Cambridge notation for atom names * atom type 3 ha added for aliphatic hydrogens * atom type 16 ct added for tetrahedral carbons * Impropers rearranged to match rtoph7 for gaunido & sidechain amide n * 2nd donor antecedants converted to CA for peptides CD for arg HE * Amide charges from Hayes and Kollman JACS 98:3335,7811 (1796) * HA charges from Wiberg and Wendoloski J. Comp. Chem. 2:53 (1981) * IC's added, and file checked, Donna Bassolino, March 1990 *
Title in the file:
* Residue Topology File for Proteins Using All Atom Hydrogens (ALLH) * Cambridge notation for atom names * atom type 3 ha added for aliphatic hydrogens * atom type 16 ct added for tetrahedral carbons * Impropers rearranged to match rtoph7 for gaunido & sidechain amide n * 2nd donor antecedants converted to CA for peptides CD for arg HE * Amide charges from Hayes and Kollman JACS 98:7811 (1796) * HA charges from Wiberg and Wendoloski J. Comp. Chem. 2:53 (1981) * IC's added, and file checked, Donna Bassolino, March 1990
This file is `RTOPALLH4' converted to the new format.
Title and comments from the run:
* Residue Topology File for Proteins Using All Atom Hydrogens (ALLH) * Cambridge notation for atom names * atom type 3 ha added for aliphatic hydrogens * atom type 16 ct added for tetrahedral carbons * Impropers rearranged to match rtoph7 for gaunido & sidechain amide n * 2nd donor antecedants converted to CA for peptides CD for arg HE * Amide charges from Hayes and Kollman JACS 98:3335,7811 (1796) * HA charges from Wiberg and Wendoloski J. Comp. Chem. 2:53 (1981) * ! ! The charges in this file were set up using the experimental formamide ! and N-methyl acetamide dipole moments of 3.7 D through the following ! proceedure. ! 1 - the C=O and N-H2 of formamide were required to be neutral ! 2 - the HA charge was arbitrarily set to zero (various Mulliken ! population analyses give it small magnitude and variable ! sign). ! 3 - The above conditions and the direction of the formamide dipole ! competely determine the formamide charges ! 4 - The CA peptide charge was arbitrarily set to 0.1 (various ! Mulliken population analysis give it 0.0 to 0.12 charges). ! 5 - The peptide charges were obtained by keeping the same C=O ! and HN charges. This requires a readjustment of the ! N charge to maintain neutrality. ! ! The resulting set of charges gives close to the same dipole moment ! when applied to N-methyl acetamide, but a somewhat different ! direction.
Title in the file:
* Residue Topology File for Proteins Using All Atom Hydrogens (ALLH) * Cambridge notation for atom names * atom type 3 ha added for aliphatic hydrogens * atom type 16 ct added for tetrahedral carbons * Impropers rearranged to match rtoph7 for gaunido & sidechain amide n * 2nd donor antecedants converted to CA for peptides CD for arg HE * Amide charges from Hayes and Kollman JACS 98:7811 (1796) * HA charges from Wiberg and Wendoloski J. Comp. Chem. 2:53 (1981)
This file is the same as `RTOPALLH3' except it has builder information for alanine added.
Title from the run:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING ALL ATOM HYDROGENS * CAMBRIDGE NOTATION FOR ATOM NAMES * ATOM TYPE 3 HA ADDED FOR ALIPHATIC HYDROGENS * ATOM TYPE 16 CT ADDED FOR TETRAHEDRAL CARBONS * BACKBONE DIHEDRALS AT 1,2,3, N IMPROPER AT 1 * DIHEDRALS REPLACED BY IMPROPERS FOR GAUNIDO & SIDECHAIN AMIDE N * IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENTS ADDED * IMPROPER DIHEDRALS INCLUDED FOR SP2 PLANAR ATOMS BUT NOT CA * DIHEDRAL AND NONBONDED EXCLUSION LISTS SORTED FOR ALL AA
Title in the file:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING ALL ATOM HYDROGENS * CAMBRIDGE NOTATION FOR ATOM NAMES * ATOM TYPE 3 HA ADDED FOR ALIPHATIC HYDROGENS * ATOM TYPE 16 CT ADDED FOR TETRAHEDRAL CARBONS * DIHEDRALS REPLACED BY IMPROPERS FOR GAUNIDO & SIDECHAIN AMIDE N * IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENTS ADDED * IMPROPER DIHEDRALS INCLUDED FOR SP2 PLANAR ATOMS BUT NOT CA * PHI,PSI,OMEGA DIHEDRALS AND NONBONDED EXCLUSION LISTS SORTED * 3/26/80 -- DAVID J. STATES
Title taken from the run which makes the file.
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING ALL ATOM HYDROGENS * CAMBRIDGE NOTATION FOR ATOM NAMES * ATOM TYPE 3 HA ADDED FOR ALIPHATIC HYDROGENS * ATOM TYPE 16 CT ADDED FOR TETRAHEDRAL CARBONS * BACKBONE DIHEDRALS AT 1,2,3, N IMPROPER AT 1 * DIHEDRALS REPLACED BY IMPROPERS FOR GAUNIDO & SIDECHAIN AMIDE N * IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENTS ADDED * IMPROPER DIHEDRALS INCLUDED FOR SP2 PLANAR ATOMS BUT NOT CA * DIHEDRAL AND NONBONDED EXCLUSION LISTS SORTED FOR ALL AA
Title in the binary file itself:
* RESIDUE TOPOLOGY FILE FOR PROTEINS USING ALL ATOM HYDROGENS * CAMBRIDGE NOTATION FOR ATOM NAMES * ATOM TYPE 3 HA ADDED FOR ALIPHATIC HYDROGENS * ATOM TYPE 16 CT ADDED FOR TETRAHEDRAL CARBONS * DIHEDRALS REPLACED BY IMPROPERS FOR GAUNIDO & SIDECHAIN AMIDE N * IMPROPER TORSIONS AND HYDROGEN DONOR ANTECEDENTS ADDED * IMPROPER DIHEDRALS INCLUDED FOR SP2 PLANAR ATOMS BUT NOT CA * PHI,PSI,OMEGA DIHEDRALS AND NONBONDED EXCLUSION LISTS SORTED * 3/26/80 -- DAVID J. STATES
The DNA topology files are largely untested. Also, they are not designed to work together with the protein topology files. These deficiencies will hopefully be corrected for version 3 of CONGEN.
Modified version of `RTOPDNA3' with charges changed and other changes.
Title in the run:
* RESIDUE TOPOLOGY FILE FOR DNA USING EXPLICIT HYDROGEN * ATOMS -- VERSION 4 -- BRB -- 2/13/82
Title in the file:
* BROMINATED CYT AND WATER ADDED 10/20/81 * RESIDUE TOPOLOGY FILE FOR DNA WITH EXPLICIT HYDROGENS * -- VERSION 4 -- BRB -- 2/13/82
Title in the run:
* RESIDUE TOPOLOGY FILE FOR DNA USING EXPLICIT HYDROGEN * ATOMS -- VERSION 2 -- BRB -- 10/20/81 * BROMINATED CYT AND WATER ADDED 10/20/81 * CONVERTED TO NEW FORMAT 10/26/81
Title in the file:
* BROMINATED CYT AND WATER ADDED 10/20/81 * RESIDUE TOPOLOGY FILE FOR DNA WITH EXPLICIT HYDROGENS * -- VERSION 2 -- BRB -- 10/20/81
Title in the topology file itself:
* DNA WITH EXPLICIT HYDROGEN TOPOLOGY FILE CREATION RUN * 1/20/81 -- BRB * READ RTF CARDS * RESIDUE TOPOLOGY FILE FOR DNA USING EXPLICIT HYDROGEN * ATOMS -- VERSION 1 -- BRB -- 1/24/81
This topology file contains all the residues needed for a DNA structure. The phosphate linkage is stored as a separate residue (PHL) and must be included in the read sequence command (where needed).
This file contains the united atom AMBER topology file. Whenever this topology file is used, you must use the automatic generation options in the GENERATE command, see section The Generate Command - Construct a Segment of the PSF, as follows:
GENERATE [segid] ANGLE TORSIONS ALL DONOR ACCEPTOR
This file is now obsolete, and is replaced by the AMBER94 topology file, which follows.
This file contains the AMBER 94 all atom topology file. There is no united atom topology file available for this parameter set. Whenever this topology file is used, the automatic generation options in the GENERATE command, see section The Generate Command - Construct a Segment of the PSF, will be turned on by default. This file must be used with the AMBER 94 parameter file, see section AMBER94PARM.
This file contains the standard amino acids, several charge variants for polar amino acids, amino and carboxy terminal amino acids, and DNA and RNA nucleotides with no terminations, terminations on each end, and single complete nucleotides. In addition, D amino acids are also present. These are generated by inverting all the construction rules for the L amino acids, so that all the chiralities are changed, including those involving just nomenclature.
Atom names in this topology file are somewhat different from those used in the previous CHARMM and CONGEN topology files. It is intended to provide closer adherence to the IUPAC naming, see section Glossary of Syntactic Terms, so that it will be easier to read Brookhaven Protein Data Bank files.
A new mechanism for patching the ends of a protein or nucleic acid is used with this topology file. The topology file stores different versions of each residue for each end as well as for interior positions. When a segment is generated, see section The Generate Command - Construct a Segment of the PSF, the appropriate end residue will be used, but the final name of the residue will be reset to the original name. Thus, the terminal residues will have the usual name, and no terminal residues, like NTER or CTER, will be used.
The URL, http://www.amber.ucsf.edu/amber/amber.html, was the source for data in this file.
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