[gmx-users] Adding Partial Charges for Small Molecules
Nancy
nancy5villa at gmail.com
Mon Jun 14 02:44:32 CEST 2010
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 "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 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
============================================================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100613/2683a19c/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: NAD.mol2
Type: application/octet-stream
Size: 7048 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100613/2683a19c/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: NAD.png
Type: image/png
Size: 9695 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100613/2683a19c/attachment.png>
More information about the gromacs.org_gmx-users
mailing list