Hi Qing,
Amber does kind of have parameters for ATP -- they are triphosphate (and
diphosphate) parameters by Dr. Carlson from 2003. You can merge these with
the sugar+base parameters from your favorite nucleic acid force field, and
that will give you Amber 'bonafide' ATP parameters. You can get them here:
http://research.bmh.manchester.ac.uk/bryce/amber/
You touched on something else important though, which is the interactions
between the gamma-phosphate and Mg2+ ions. Panteva from Dr. York's group
showed that the 'vanilla' ion parameters typically overestimate the
interactions between nucleic acid phosphates and divalent ions. They
reparameterized them to create a modified 12-6-4 (m12-6-4). They didn't do
the same test with the triphosphate parameters, but my own (non-published)
tests have shown that the interaction between the ions and the triphosphate
tail are also overestimated.
It's been on my to-do list to tune the interaction between the two to get
more accurate interaction energies, but in the meantime a suitable
approximation might be to fiddle with Panteva's m12-6-4 parameters to get
them to apply to the triphosphate oxygen atoms, which should give you more
balanced interactions (though not perfect -- whatever that may be).
Hope that helps.
Regards,
Zachary
On Fri, Nov 22, 2019 at 1:12 PM Qing Lv <lvqingjiejie.163.com> wrote:
> 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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>
--
Zachary Fallon, PhD Candidate
Dr. Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (914) 703-1010 <(914)+703+1010> Email: zachary.fallon.stonybrook.
<zachary.fallon.stonybrook.edu>edu
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Received on Fri Nov 22 2019 - 10:30:02 PST
