Hi All,<br><br>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 "AM1-BCC" method are generally of greater magnitude compared to charges assigned using the Gasteiger method.<br>
<br>What is a good way to add correct partial charges to a small molecule?<br><br>The mol2 structure code (with incorrect Gasteiger charges) is written below (and attached as NAD.mol2 with corresponding PNG structure image).<br>
<br>Thanks in advance,<br>Nancy<br><br>============================================================================<br>@<TRIPOS>MOLECULE<br>NAD.mol2<br> 70 74 1 0 0<br>SMALL<br>USER_CHARGES<br><br><br>
@<TRIPOS>ATOM<br> 1 C1 -1.4117 5.8700 -3.4377 C.2 1 LIG1 -0.0471<br> 2 C2 -0.2808 5.1989 -2.9922 C.2 1 LIG1 -0.0472<br> 3 C3 0.0698 5.2540 -1.6463 C.2 1 LIG1 -0.0021<br>
4 N1 -0.7125 5.8930 -0.7233 N.2 1 LIG1 -0.2845<br> 5 C4 -1.7621 6.6431 -1.1880 C.2 1 LIG1 0.0105<br> 6 C5 -2.1590 6.6215 -2.5315 C.2 1 LIG1 0.0510<br>
7 C6 -3.3433 7.3892 -2.9991 C.2 1 LIG1 0.2416<br> 8 O1 -3.7255 7.3875 -4.2002 O.2 1 LIG1 -0.2721<br> 9 N2 -4.0978 8.1475 -2.0847 N.3 1 LIG1 -0.3250<br>
10 O2 0.0324 4.4339 0.9916 O.3 1 LIG1 -0.3484<br> 11 C7 -1.0355 3.6965 1.6402 C.3 1 LIG1 0.1165<br> 12 C8 -1.4243 2.4599 0.8071 C.3 1 LIG1 0.1276<br>
13 O3 -0.4100 1.4351 0.9207 O.3 1 LIG1 -0.1602<br> 14 P1 0.8613 1.4216 -0.0633 P.3 1 LIG1 0.5624<br> 15 O4 2.0180 2.1020 0.5580 O.2 1 LIG1 -0.3429<br>
16 O5 0.5634 2.0116 -1.3891 O.3 1 LIG1 -0.3429<br> 17 O6 1.1223 -0.1529 -0.1877 O.3 1 LIG1 0.0575<br> 18 P2 0.0541 -1.2893 -0.5527 P.3 1 LIG1 0.5624<br>
19 O7 -1.1823 -1.2052 0.2607 O.3 1 LIG1 -0.3429<br> 20 O8 0.6340 -2.6390 -0.3765 O.2 1 LIG1 -0.3429<br> 21 O9 -0.2208 -1.0077 -2.1109 O.3 1 LIG1 -0.1602<br>
22 O10 -2.0844 -2.0838 -4.0533 O.3 1 LIG1 -0.3483<br> 23 C9 -1.7580 -0.6726 -3.9721 C.3 1 LIG1 0.1165<br> 24 C10 -1.4291 -0.3206 -2.5098 C.3 1 LIG1 0.1276<br>
25 N3 -5.5165 -1.9977 -1.1853 N.2 1 LIG1 -0.2341<br> 26 C11 -5.3009 -1.7637 -2.4944 C.2 1 LIG1 0.0912<br> 27 N4 -4.1259 -2.3733 -2.8716 N.3 1 LIG1 -0.2445<br>
28 C12 -3.5825 -3.0679 -1.8327 C.2 1 LIG1 0.1583<br> 29 C13 -4.4622 -2.7976 -0.7674 C.2 1 LIG1 0.1418<br> 30 N5 -2.5159 -3.8010 -1.6563 N.2 1 LIG1 -0.2186<br>
31 C14 -2.2518 -4.3018 -0.4707 C.2 1 LIG1 0.1192<br> 32 N6 -3.0604 -4.0697 0.5431 N.2 1 LIG1 -0.2228<br> 33 C15 -4.1365 -3.3442 0.4336 C.2 1 LIG1 0.1340<br>
34 N7 -4.8438 -3.2010 1.5627 N.3 1 LIG1 -0.2849<br> 35 C16 -2.1891 4.7099 1.7524 C.3 1 LIG1 0.1128<br> 36 C17 -1.4568 6.0605 1.7533 C.3 1 LIG1 0.1256<br>
37 C18 -0.3444 5.8071 0.7094 C.3 1 LIG1 0.1560<br> 38 C19 -3.0362 0.0509 -4.4501 C.3 1 LIG1 0.1128<br> 39 C20 -3.9053 -1.0632 -5.0633 C.3 1 LIG1 0.1257<br>
40 C21 -3.5098 -2.2874 -4.2107 C.3 1 LIG1 0.1588<br> 41 O11 -2.9991 4.5200 2.9209 O.3 1 LIG1 -0.3874<br> 42 O12 -0.8413 6.3227 3.0256 O.3 1 LIG1 -0.3858<br>
43 O13 -3.5425 -1.3145 -6.4282 O.3 1 LIG1 -0.3858<br> 44 O14 -2.7472 1.1126 -5.3700 O.3 1 LIG1 -0.3874<br> 45 H1 -1.6809 5.8357 -4.4909 H 1 LIG1 0.0632<br>
46 H2 0.3396 4.6461 -3.6934 H 1 LIG1 0.0636<br> 47 H3 0.9656 4.7572 -1.2733 H 1 LIG1 0.0793<br> 48 H4 -2.2796 7.2615 -0.4632 H 1 LIG1 0.0801<br>
49 H5 -4.8503 8.7190 -2.4374 H 1 LIG1 0.1458<br> 50 H6 -3.7587 8.2854 -1.1465 H 1 LIG1 0.1458<br> 51 H7 -0.6981 3.4004 2.6380 H 1 LIG1 0.0660<br>
52 H8 -1.5845 2.7299 -0.2407 H 1 LIG1 0.0645<br> 53 H9 -2.3510 2.0430 1.2095 H 1 LIG1 0.0645<br> 54 H10 -0.9095 -0.4615 -4.6296 H 1 LIG1 0.0660<br>
55 H11 -1.2870 0.7565 -2.4090 H 1 LIG1 0.0645<br> 56 H12 -2.2603 -0.6329 -1.8739 H 1 LIG1 0.0645<br> 57 H13 -5.9324 -1.1833 -3.1491 H 1 LIG1 0.1018<br>
58 H14 -1.3609 -4.8928 -0.3242 H 1 LIG1 0.1064<br> 59 H15 -4.6910 -3.8437 2.3366 H 1 LIG1 0.1259<br> 60 H16 -5.8375 -2.9879 1.5154 H 1 LIG1 0.1259<br>
61 H17 -2.8150 4.6581 0.8568 H 1 LIG1 0.0659<br> 62 H18 -2.1232 6.8857 1.5028 H 1 LIG1 0.0675<br> 63 H19 0.5295 6.4594 0.8618 H 1 LIG1 0.0853<br>
64 H20 -3.5627 0.4623 -3.5840 H 1 LIG1 0.0659<br> 65 H21 -4.9700 -0.8302 -5.0011 H 1 LIG1 0.0675<br> 66 H22 -3.6913 -3.2429 -4.7274 H 1 LIG1 0.0854<br>
67 H23 -3.4491 3.6578 2.8683 H 1 LIG1 0.2107<br> 68 H24 -0.3142 7.1392 2.9619 H 1 LIG1 0.2108<br> 69 H25 -3.3167 -0.4612 -6.8446 H 1 LIG1 0.2108<br>
70 H26 -3.5789 1.5634 -5.6077 H 1 LIG1 0.2107<br>@<TRIPOS>BOND<br> 1 1 45 1<br> 2 1 2 ar<br> 3 1 6 ar<br> 4 2 46 1<br> 5 2 3 ar<br> 6 3 47 1<br>
7 3 4 ar<br> 8 4 5 ar<br> 9 5 48 1<br> 10 5 6 ar<br> 11 6 7 1<br> 12 7 9 am<br> 13 7 8 2<br> 14 9 50 1<br> 15 9 49 1<br> 16 10 11 1<br>
17 10 37 1<br> 18 11 35 1<br> 19 11 51 1<br> 20 11 12 1<br> 21 12 53 1<br> 22 12 52 1<br> 23 12 13 1<br> 24 13 14 1<br> 25 14 17 1<br> 26 14 16 1<br> 27 14 15 1<br>
28 17 18 1<br> 29 18 21 1<br> 30 18 20 1<br> 31 18 19 1<br> 32 22 40 1<br> 33 22 23 1<br> 34 23 24 1<br> 35 23 54 1<br> 36 23 38 1<br> 37 24 21 1<br> 38 24 56 1<br>
39 24 55 1<br> 40 25 29 ar<br> 41 25 26 ar<br> 42 26 57 1<br> 43 26 27 ar<br> 44 27 28 ar<br> 45 28 30 ar<br> 46 29 33 ar<br> 47 29 28 ar<br> 48 30 31 ar<br>
49 31 58 1<br> 50 31 32 ar<br> 51 32 33 ar<br> 52 33 34 1<br> 53 34 60 1<br> 54 34 59 1<br> 55 35 36 1<br> 56 35 61 1<br> 57 35 41 1<br> 58 36 37 1<br>
59 36 62 1<br> 60 36 42 1<br> 61 37 4 1<br> 62 37 63 1<br> 63 38 64 1<br> 64 38 44 1<br> 65 38 39 1<br> 66 39 65 1<br> 67 39 43 1<br> 68 39 40 1<br> 69 40 27 1<br>
70 40 66 1<br> 71 41 67 1<br> 72 42 68 1<br> 73 43 69 1<br> 74 44 70 1<br>@<TRIPOS>SUBSTRUCTURE<br> 1 LIG1 1 GROUP 1 LIG 1<br>============================================================================<br>
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