A.5 All Hydrogen Topology Files

A.5.1 RTOPALLH6

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