2 ; Column 1 : default bondtype
3 ; Column 2 : default angletype
4 ; Column 3 : default proper dihedraltype
5 ; Column 4 : default improper dihedraltype
6 ; Column 5 : This controls the generation of dihedrals from the bonding.
7 ; All possible dihedrals are generated automatically. A value of
8 ; 1 here means that all these are retained. A value of
9 ; 0 here requires generated dihedrals be removed if
10 ; * there are any dihedrals on the same central atoms
11 ; specified in the residue topology, or
12 ; * there are other identical generated dihedrals
13 ; sharing the same central atoms, or
14 ; * there are other generated dihedrals sharing the
15 ; same central bond that have fewer hydrogen atoms
16 ; Column 6 : number of neighbors to exclude from non-bonded interactions
17 ; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
18 ; 0 = do not generate such
19 ; Column 8 : 1 = remove proper dihedrals if found centered on the same
20 ; bond as an improper dihedral
21 ; 0 = do not generate such
22 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
25 ; now: water, ions, urea, terminal caps, AA's and terminal AA's
48 [ IB+ ] ; big positive ion
88 [ URE ] ; urea added in by EJS, resp charges by Jim Caldwell
170 ; Next are non-terminal AA's
199 [ GLY ] ; HAx atoms assigned new ff03 atom type
1000 [ ORN ] ; charges taken from amber99.prm of tinker 4.0
1045 [ DAB ] ; sidechain charges fit to maintain heavy atom charge group trend LYS -> ORN -> DAB
1169 [ HYP ] ; S Park, R J Radmer, T E Klein & V S Pande (submitted).
1331 ; non-terminal acidic AA's
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