Thank you so much, Zachary. This is very helpful.
Best,
Qing
At 2019-11-23 02:26:28, "Zachary Fallon" <zachary.fallon.stonybrook.edu> wrote:
>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 - 22:30:02 PST
