[gmx-users] Adding Partial Charges for Small Molecules

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 14 02:54:25 CEST 2010



Nancy wrote:
> Hi All,
> 
> I am trying to add partial charges to nicotinamide adenine dinucleotide 
> (NAD+), for input to molecular simulations.  I have been using the UCSF 
> Chimera program to do this.  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 

Sounds like a known issue with Chimera...

http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001732.html

> "AM1-BCC" method are generally of greater magnitude compared to charges 
> assigned using the Gasteiger method.
> 
> What is a good way to add correct partial charges to a small molecule?
> 

The best way is to follow the original methodology of the force field itself. 
The antechamber program of Amber is probably a good place to start to get 
Amber-compatible topologies.  Also have a look here:

http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

All of the above will require conversion to Gromacs-compatible formats, but 
there are scripts on the User Contribution site that might be suitable.

-Justin

> 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
> ============================================================================
> 
> 
> 
> ------------------------------------------------------------------------
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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