Hi Justin,<br><br>Thanks for the useful info.<br><br>Nancy<br><br><br><br><div class="gmail_quote">On Sun, Jun 13, 2010 at 8:54 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Nancy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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 <br>
</blockquote>
<br></div>
Sounds like a known issue with Chimera...<br>
<br>
<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001732.html" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001732.html</a><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
"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>
</blockquote>
<br></div>
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:<br>
<br>
<a href="http://www.pharmacy.manchester.ac.uk/bryce/amber#cof" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/amber#cof</a><br>
<br>
All of the above will require conversion to Gromacs-compatible formats, but there are scripts on the User Contribution site that might be suitable.<br><font color="#888888">
<br>
-Justin<br>
<br>
</font><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
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>
<br>
<br>
<br></div></div>
------------------------------------------------------------------------<br>
<br>
</blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
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