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   macroModel atom types

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

MacroModel Atom Types

        MacroModel - Atom and Bond Type Description and Numbering
        ---------- - --------------------------------------------

BONDS:
No Symbol    Description
-- ------  --------------
 0   .     Zero order bond
 1   -     Single Bond
 2   =     Double Bond
 3   %     Triple Bond
 4   *     Bond of Undefined Order 

ATOMS:
No Symbol    Description                       Equivalencies
-- ------    -----------                       -------------
                                     MM2   Charmm   Amber     
 1   C1   Carbon - SP                 4                     
 2   C2   C - SP2                    2,3    CT,C   C,C*,CA,   
                                                   CB,CC,CM, 
                                                   CF,CG,CN
 3   C3   C - SP3                     1      CT       CT       
 4   CA   United atom CH -  SP3             CH1E      CH       
 5   CB   United atom CH2 - SP3             CH2E      C2       
 6   CC   United atom CH3 - SP3             CH3E      C3       
 7   CD   United atom CH -  SP2             CR1E   CD,CE,      
                                                   CI,CJ,CP
 8   CE   United atom CH2 - SP2
 9   CF   United atom CH -  SP
10
11
12
13
14   C0   Any Carbon
15   O2   Oxygen - Double Bond        7     O         O,O2     
16   O3   O - Single Bonds            6    OH1,OH2   OS,OH     
17   OA   United atom OH                   OH1E                
18   OM   O- (alkoxide, carboxylate) 25    OC 
19   OW   United atom H2O - Water          OH2E
20
21
22
23   O0   Any Oxygen
24   N1   Nitrogen - SP              10
25   N2   N - SP2                     9   N,NR,NP,   N,NB,NC   
                                          NH1,NH2    N*,N2
26   N3   N - SP3                     8     NH3        NT      
27   NA   United atom NH -  SP3                            
28   NB   United atom NH2 - SP3
29   NC   United atom NH -  SP2             NH1E
30   ND   United atom NH2 - SP2             NH2E
31   N4   N+ - SP2                          NC2         NA     
32   N5   N+ - SP3                                      N3     
33   NE   United atom NH+ -  SP3
34   NF   United atom NH2+ - SP3              
35   NG   United atom NH3+ - SP3            NH3E
36   NH   United atom NH+ -  SP2
37   NI   United atom NH2+ - SP2            NC2E
38
39
40   N0   Any Nitrogen
41   H1   H-Electroneut (e.g. C,S)    5      HA       HC,HS    
42   H2   H-O(Neut)                 21,24   H,HC        HO     
43   H3   H-N(Neut)                  23     H,HC       H,H2    
44   H4   H-Cation                                      H3     
45   H5   H-Anion
46
47
48   H0   Any Hydrogen                                         
49   S1   Sulfur                     15       S        S,SH    
50   SA   United atom SH                     SH1E
51   SM   S- (thiolate anion)
52   S0   Any Sulfur                          S                
53   P0   Phosphorus                 29                   P
54
55
56   F0   Fluorine                   11
57   Cl   Chlorine                   12
58   Br   Bromine                    13
59   I0   Iodine                     14
60   Si   Silicon                    19
61
62   Z0   Special Atom to be defined
63   Lp   Lone Electron Pair         20                  LP
64   00   Any Atom                    0         *

        Note: 00 atoms stored as type 0 in atom connection table.
        Note: All current force fields require explicit hydrogens
                on heteroatoms.




© Goodman Group, 2005-2017; privacy; last updated November 16, 2017

department of chemistry University of Cambridge