[Chimera-users] Adding Partial Charges

Nancy nancy5villa at gmail.com
Sun Jun 13 17:40:25 PDT 2010


Hi All,

I am trying to add charges to nicotinamide adenine dinucleotide (NAD+) using
UCSF Chimera; the total charge on this molecule should be -1 (assuming the
ionization of NAD+ at pH ~7.0, see attached figure).  When I add Gasteiger
charges, the total charge sums up incorrectly to 0, even though the net
charge specified in the drop-down box is -1.  However, using the "AM1-BCC"
method, the net charge correctly sums up to -1.  The charge model used is
"Amber ff99SB".  I have also noticed that the partial charges on individual
atoms assigned when using the "AM1-BCC" method are generally of greater
magnitude compared to charges assigned using the Gasteiger method.

I am wondering why the Gasteiger method assigns an incorrect net charge in
the case of NAD+.

The mol2 structure code (with incorrect Gasteiger charges) is written below
(and attached as NAD.mol2 with corresponding PNG structure image).

Thanks in advance,
Nancy

============================================================================
@<TRIPOS>MOLECULE
NAD.mol2
   70    74    1     0     0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C1         -1.4117    5.8700   -3.4377 C.2       1     LIG1
-0.0471
      2 C2         -0.2808    5.1989   -2.9922 C.2       1     LIG1
-0.0472
      3 C3          0.0698    5.2540   -1.6463 C.2       1     LIG1
-0.0021
      4 N1         -0.7125    5.8930   -0.7233 N.2       1     LIG1
-0.2845
      5 C4         -1.7621    6.6431   -1.1880 C.2       1     LIG1
0.0105
      6 C5         -2.1590    6.6215   -2.5315 C.2       1     LIG1
0.0510
      7 C6         -3.3433    7.3892   -2.9991 C.2       1     LIG1
0.2416
      8 O1         -3.7255    7.3875   -4.2002 O.2       1     LIG1
-0.2721
      9 N2         -4.0978    8.1475   -2.0847 N.3       1     LIG1
-0.3250
     10 O2          0.0324    4.4339    0.9916 O.3       1     LIG1
-0.3484
     11 C7         -1.0355    3.6965    1.6402 C.3       1     LIG1
0.1165
     12 C8         -1.4243    2.4599    0.8071 C.3       1     LIG1
0.1276
     13 O3         -0.4100    1.4351    0.9207 O.3       1     LIG1
-0.1602
     14 P1          0.8613    1.4216   -0.0633 P.3       1     LIG1
0.5624
     15 O4          2.0180    2.1020    0.5580 O.2       1     LIG1
-0.3429
     16 O5          0.5634    2.0116   -1.3891 O.3       1     LIG1
-0.3429
     17 O6          1.1223   -0.1529   -0.1877 O.3       1     LIG1
0.0575
     18 P2          0.0541   -1.2893   -0.5527 P.3       1     LIG1
0.5624
     19 O7         -1.1823   -1.2052    0.2607 O.3       1     LIG1
-0.3429
     20 O8          0.6340   -2.6390   -0.3765 O.2       1     LIG1
-0.3429
     21 O9         -0.2208   -1.0077   -2.1109 O.3       1     LIG1
-0.1602
     22 O10        -2.0844   -2.0838   -4.0533 O.3       1     LIG1
-0.3483
     23 C9         -1.7580   -0.6726   -3.9721 C.3       1     LIG1
0.1165
     24 C10        -1.4291   -0.3206   -2.5098 C.3       1     LIG1
0.1276
     25 N3         -5.5165   -1.9977   -1.1853 N.2       1     LIG1
-0.2341
     26 C11        -5.3009   -1.7637   -2.4944 C.2       1     LIG1
0.0912
     27 N4         -4.1259   -2.3733   -2.8716 N.3       1     LIG1
-0.2445
     28 C12        -3.5825   -3.0679   -1.8327 C.2       1     LIG1
0.1583
     29 C13        -4.4622   -2.7976   -0.7674 C.2       1     LIG1
0.1418
     30 N5         -2.5159   -3.8010   -1.6563 N.2       1     LIG1
-0.2186
     31 C14        -2.2518   -4.3018   -0.4707 C.2       1     LIG1
0.1192
     32 N6         -3.0604   -4.0697    0.5431 N.2       1     LIG1
-0.2228
     33 C15        -4.1365   -3.3442    0.4336 C.2       1     LIG1
0.1340
     34 N7         -4.8438   -3.2010    1.5627 N.3       1     LIG1
-0.2849
     35 C16        -2.1891    4.7099    1.7524 C.3       1     LIG1
0.1128
     36 C17        -1.4568    6.0605    1.7533 C.3       1     LIG1
0.1256
     37 C18        -0.3444    5.8071    0.7094 C.3       1     LIG1
0.1560
     38 C19        -3.0362    0.0509   -4.4501 C.3       1     LIG1
0.1128
     39 C20        -3.9053   -1.0632   -5.0633 C.3       1     LIG1
0.1257
     40 C21        -3.5098   -2.2874   -4.2107 C.3       1     LIG1
0.1588
     41 O11        -2.9991    4.5200    2.9209 O.3       1     LIG1
-0.3874
     42 O12        -0.8413    6.3227    3.0256 O.3       1     LIG1
-0.3858
     43 O13        -3.5425   -1.3145   -6.4282 O.3       1     LIG1
-0.3858
     44 O14        -2.7472    1.1126   -5.3700 O.3       1     LIG1
-0.3874
     45 H1         -1.6809    5.8357   -4.4909 H         1     LIG1
0.0632
     46 H2          0.3396    4.6461   -3.6934 H         1     LIG1
0.0636
     47 H3          0.9656    4.7572   -1.2733 H         1     LIG1
0.0793
     48 H4         -2.2796    7.2615   -0.4632 H         1     LIG1
0.0801
     49 H5         -4.8503    8.7190   -2.4374 H         1     LIG1
0.1458
     50 H6         -3.7587    8.2854   -1.1465 H         1     LIG1
0.1458
     51 H7         -0.6981    3.4004    2.6380 H         1     LIG1
0.0660
     52 H8         -1.5845    2.7299   -0.2407 H         1     LIG1
0.0645
     53 H9         -2.3510    2.0430    1.2095 H         1     LIG1
0.0645
     54 H10        -0.9095   -0.4615   -4.6296 H         1     LIG1
0.0660
     55 H11        -1.2870    0.7565   -2.4090 H         1     LIG1
0.0645
     56 H12        -2.2603   -0.6329   -1.8739 H         1     LIG1
0.0645
     57 H13        -5.9324   -1.1833   -3.1491 H         1     LIG1
0.1018
     58 H14        -1.3609   -4.8928   -0.3242 H         1     LIG1
0.1064
     59 H15        -4.6910   -3.8437    2.3366 H         1     LIG1
0.1259
     60 H16        -5.8375   -2.9879    1.5154 H         1     LIG1
0.1259
     61 H17        -2.8150    4.6581    0.8568 H         1     LIG1
0.0659
     62 H18        -2.1232    6.8857    1.5028 H         1     LIG1
0.0675
     63 H19         0.5295    6.4594    0.8618 H         1     LIG1
0.0853
     64 H20        -3.5627    0.4623   -3.5840 H         1     LIG1
0.0659
     65 H21        -4.9700   -0.8302   -5.0011 H         1     LIG1
0.0675
     66 H22        -3.6913   -3.2429   -4.7274 H         1     LIG1
0.0854
     67 H23        -3.4491    3.6578    2.8683 H         1     LIG1
0.2107
     68 H24        -0.3142    7.1392    2.9619 H         1     LIG1
0.2108
     69 H25        -3.3167   -0.4612   -6.8446 H         1     LIG1
0.2108
     70 H26        -3.5789    1.5634   -5.6077 H         1     LIG1
0.2107
@<TRIPOS>BOND
     1    1   45 1
     2    1    2 ar
     3    1    6 ar
     4    2   46 1
     5    2    3 ar
     6    3   47 1
     7    3    4 ar
     8    4    5 ar
     9    5   48 1
    10    5    6 ar
    11    6    7 1
    12    7    9 am
    13    7    8 2
    14    9   50 1
    15    9   49 1
    16   10   11 1
    17   10   37 1
    18   11   35 1
    19   11   51 1
    20   11   12 1
    21   12   53 1
    22   12   52 1
    23   12   13 1
    24   13   14 1
    25   14   17 1
    26   14   16 1
    27   14   15 1
    28   17   18 1
    29   18   21 1
    30   18   20 1
    31   18   19 1
    32   22   40 1
    33   22   23 1
    34   23   24 1
    35   23   54 1
    36   23   38 1
    37   24   21 1
    38   24   56 1
    39   24   55 1
    40   25   29 ar
    41   25   26 ar
    42   26   57 1
    43   26   27 ar
    44   27   28 ar
    45   28   30 ar
    46   29   33 ar
    47   29   28 ar
    48   30   31 ar
    49   31   58 1
    50   31   32 ar
    51   32   33 ar
    52   33   34 1
    53   34   60 1
    54   34   59 1
    55   35   36 1
    56   35   61 1
    57   35   41 1
    58   36   37 1
    59   36   62 1
    60   36   42 1
    61   37    4 1
    62   37   63 1
    63   38   64 1
    64   38   44 1
    65   38   39 1
    66   39   65 1
    67   39   43 1
    68   39   40 1
    69   40   27 1
    70   40   66 1
    71   41   67 1
    72   42   68 1
    73   43   69 1
    74   44   70 1
@<TRIPOS>SUBSTRUCTURE
     1     LIG1    1   GROUP 1   LIG 1
============================================================================
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