Next: RTOPALLH6, Up: Residue Topology Files
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