Dear Colleagues,
I am using Amber 18 to simulate an enzyme complexed with ATP and Mg2+. It seems that Amber does not have the parameters of ATP and so I generated them using Antechamber. However, at the beginning of the simulation, the terminal phosphate of ATP became somewhat distorted (one oxygen atom bends reversely to approach the Mg2+, and makes the P atom a vertex of the pyramid). Apparently, this is due to the strong electrostatic attractions between O- and Mg2+; but is this reasonable?
I wonder if my ATP force field parameters are wrong. Below is the MOL2 file generated by Antechamber (the atom charges are RESP calculated at M06-2X/6-31+G* level):
.<TRIPOS>MOLECULE
ATP
43 45 1 0 0
SMALL
resp
.<TRIPOS>ATOM
1 P1 -1.9480 -0.7930 1.6560 p5 1 ATP 1.70903 6
2 P2 -3.9820 0.0420 -0.4940 p5 1 ATP 1.72489 6
3 P3 -7.0290 -0.3220 -0.7710 p5 1 ATP 1.98614 8
4 O1 1.7270 0.2490 0.7220 os 1 ATP -0.28453 3
5 O2 3.6660 2.4450 -1.3200 oh 1 ATP -0.75654 4
6 O3 2.2930 3.5310 0.6030 oh 1 ATP -0.76155 0
7 O4 -0.9540 0.3960 1.8460 os 1 ATP -0.62000 0
8 O5 -3.3080 -0.5270 0.8750 os 1 ATP -0.71217 6
9 O6 -1.0520 -1.9470 1.1060 o 1 ATP -0.99528 1
10 O7 -2.3110 -1.1090 3.1460 o 1 ATP -0.99528 1
11 O8 -5.5690 0.3180 -0.6240 os 1 ATP -0.84173 5
12 O9 -3.3970 -0.7850 -1.6900 o 1 ATP -0.97134 7
13 O10 -3.2650 1.4440 -0.6120 o 1 ATP -0.97134 7
14 O11 -8.0300 0.7990 -0.3410 o 1 ATP -1.02310 5
15 O12 -7.4420 -0.6960 -2.2360 o 1 ATP -1.02310 5
16 O13 -7.3470 -1.5500 0.1420 o 1 ATP -1.02310 5
17 N1 3.9060 -0.3840 -0.0640 na 1 ATP 0.45657 0
18 N2 4.8420 -2.3670 -0.6140 nc 1 ATP -0.46686 1
19 N3 6.0210 0.8880 0.0380 nb 1 ATP -0.77590 6
20 N4 8.0310 -0.3700 -0.4160 nb 1 ATP -1.09160 7
21 N5 7.9000 -2.6240 -0.9040 nh 1 ATP -0.79829 9
22 C1 2.6090 1.6650 -0.7840 c3 1 ATP 0.49345 4
23 C2 1.5590 2.4870 -0.0840 c3 1 ATP 0.08337 7
24 C3 2.9860 0.6990 0.3260 c3 1 ATP -0.27733 3
25 C4 0.9200 1.4140 0.8620 c3 1 ATP 0.28507 8
26 C5 -0.5690 1.0760 0.6680 c3 1 ATP 0.05620 8
27 C6 5.2730 -0.2060 -0.1680 ca 1 ATP 0.15060 8
28 C7 3.6930 -1.6870 -0.3400 cd 1 ATP -0.24962 7
29 C8 5.8670 -1.4400 -0.4960 ca 1 ATP 0.13777 0
30 C9 7.2480 -1.4690 -0.6050 ca 1 ATP 0.81916 8
31 C10 7.3330 0.7580 -0.1030 ca 1 ATP 0.85918 1
32 H1 2.1500 1.1080 -1.6040 h1 1 ATP 0.02081 1
33 H2 0.8500 2.8960 -0.8150 h1 1 ATP 0.05845 4
34 H3 3.4230 1.2180 1.1820 h2 1 ATP 0.14264 0
35 H4 1.0150 1.7420 1.8970 h1 1 ATP 0.05036 7
36 H5 -0.7580 0.4610 -0.2160 h1 1 ATP 0.07843 3
37 H6 -1.1700 1.9810 0.5960 h1 1 ATP 0.07843 3
38 H7 4.0850 2.9000 -0.5900 ho 1 ATP 0.47591 5
39 H8 1.5820 3.9550 1.0900 ho 1 ATP 0.42047 5
40 H9 2.6880 -2.1050 -0.3310 h5 1 ATP 0.30583 4
41 H10 7.8750 1.6750 0.0560 h5 1 ATP -0.10002 6
42 H11 7.2590 -3.3940 -0.9960 hn 1 ATP 0.17295 6
43 H12 8.8940 -2.6820 -1.0150 hn 1 ATP 0.17295 6
.<TRIPOS>BOND
1 1 7 1
2 1 8 1
3 1 9 1
4 1 10 1
5 2 8 1
6 2 11 1
7 2 12 1
8 2 13 1
9 3 11 1
10 3 14 1
11 3 15 1
12 3 16 1
13 4 24 1
14 4 25 1
15 5 22 1
16 5 38 1
17 6 23 1
18 6 39 1
19 7 26 1
20 17 24 1
21 17 27 1
22 17 28 1
23 18 28 2
24 18 29 1
25 19 27 ar
26 19 31 ar
27 20 30 ar
28 20 31 ar
29 21 30 1
30 21 42 1
31 21 43 1
32 22 23 1
33 22 24 1
34 22 32 1
35 23 25 1
36 23 33 1
37 24 34 1
38 25 26 1
39 25 35 1
40 26 36 1
41 26 37 1
42 27 29 ar
43 28 40 1
44 29 30 ar
45 31 41 1
.<TRIPOS>SUBSTRUCTURE
1 ATP 1 TEMP 0 **** **** 0 ROOT
Are there any problems in the ATP parameters? Or, are there any well-established force field parameters of ATP available?
Thanks a lot,
Qing
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Received on Fri Nov 22 2019 - 10:30:02 PST
