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    This document contains two tables that describe basic atom types and special atom types used in the General Amber Force Field (GAFF). Table I(a) lists common atom types such as sp2 and sp3 carbons, nitrogens, oxygens, and halogens along with their descriptions. Table I(b) describes special atom types that account for substituents, conjugation, and ring membership for atoms like carbons, nitrogens, and phosphorus. These atom types are assigned specific force field parameters in GAFF to model different hybridizations and chemical environments.

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    GAFF atom types

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    This document contains two tables that describe basic atom types and special atom types used in the General Amber Force Field (GAFF). Table I(a) lists common atom types such as sp2 and sp3 carbons, nitrogens, oxygens, and halogens along with their descriptions. Table I(b) describes special atom types that account for substituents, conjugation, and ring membership for atoms like carbons, nitrogens, and phosphorus. These atom types are assigned specific force field parameters in GAFF to model different hybridizations and chemical environments.

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    125 views1 page

    GAFF Atom Types

    Uploaded by

    meny
    This document contains two tables that describe basic atom types and special atom types used in the General Amber Force Field (GAFF). Table I(a) lists common atom types such as sp2 and sp3 carbons, nitrogens, oxygens, and halogens along with their descriptions. Table I(b) describes special atom types that account for substituents, conjugation, and ring membership for atoms like carbons, nitrogens, and phosphorus. These atom types are assigned specific force field parameters in GAFF to model different hybridizations and chemical environments.

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    of 1

    Table I (a).

    Basic Atom Types in GAFF


    Atom type

    Description

    Atom type

    Description

    c
    c1
    c2
    c3
    ca

    sp2 C in C=O, C=S


    sp1 C
    sp2 C, aliphatic
    sp3 C
    sp2 C, aromatic

    o
    oh
    os

    sp2 O in C=O, COOsp3 O in hydroxyl group


    sp3 O in ether and ester

    n
    n1
    n2

    sp2 N in amide
    sp1 N
    sp2 N with 2 subst.
    readl double bond
    sp3 N with 3 subst.
    sp3 N with 4 subst.
    sp2 N with 3 subst
    amine N connected
    to the aromatic rings
    N in nitro group

    s2
    sh
    ss
    s4
    s6

    sp2 S (p=S, C=S etc)


    sp3 S in thiol group
    sp3 S in -SR and SS
    hypervalent S, 3 subst.
    hypervalent S, 4 subst.

    hc
    ha
    hn
    ho
    hs
    hp

    H on aliphatic C
    H on aromatic C
    H on N
    H on O
    H on S
    H on P

    any F
    any Cl
    any Br
    any I

    p2
    p3
    p4
    p5

    sp2 P (C=P etc)


    sp3 P, 3 subst.
    hypervalent P, 3 subst.
    hypervalent P, 4 subst.

    n3
    n4
    na
    nh
    no
    f
    cl
    br
    i

    Table I (b). Special Atom Types in GAFF


    Atom type

    Description

    Atom type

    Description

    h1
    h2
    h3
    h4
    h5

    H on aliphatic C with 1 EW group;


    H on aliphatic C with 2 EW group;
    H on aliphatic C with 3 EW group;
    H on aromatic C with 4 EW group;
    H on aromatic C with 5 EW group;

    cc(cd)
    ce(cf)
    cp(cq)
    cu
    cv
    cx
    cy

    inner sp2 C in conj. ring systems


    inner sp2 C in conj. chain systems
    bridge aromatic C
    sp2 C in three-memberred rings
    sp2 C in four-memberred rings
    sp3 C in three-memberred rings
    sp3 C in four-memberred rings

    n
    nb
    nc(nd)
    sx
    sy

    aromatic nitrogen
    inner sp2 N in conj. ring systems
    inner sp2 N in conj. chain systems
    conj. S, 3 subst.
    conj. S, 4 subst.

    pb
    pc(pd)
    pe(pf)
    px
    py

    aromatic phosphorus
    inner sp2 P in conj. ring systems
    inner sp2 P in conj. chain systems
    conj. P, 3 subst.
    conj. P, 4 subst.

    EW: electron-withdraw group

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