I gotcha thank you very much Carlos !
So I changed it to the TIP3P in my script.
So finally for my educational purposes, would it be possible to refine here
one or two pdb references containing DNA (better in complex with protein)
which 100% would work with the tleap parametrization ? I still have not
found any solution ..
Yours with thanks
Enrico
Il giorno lun 22 apr 2024 alle ore 17:39 Carlos Simmerling <
carlos.simmerling.stonybrook.edu> ha scritto:
>
>
> On Mon, Apr 22, 2024 at 11:13 AM Enrico Martinez <jmsstarlight.gmail.com>
> wrote:
>
>> Okay, thank you very much Carlos !
>>
>> Yes of course, for the purposes of this tutorial I would prefer to just
>> cut the residues with missed atoms. By the way, it's strange that I
>> proposed the structure with pdb4amber with --fixmissed, but it reported
>> nothing. Also, tleap added these missed atoms (as it does for missed
>> oxygens for example) but does not recognise them in the next steps. So I
>> still a bit in the suck...
>>
>
> tleap should not add missing atoms that are not in the residue
> definitions. The messages "created a new atom" about reading those atoms
> in the file for that residue, and then it can't find parameters since they
> are not in the library for it. If you delete them the errors will go away.
>
>
>> BTW which parameters will be used if I source the water as OPC but then
>> solvate the whole system using TIP3P ??
>>
>
> OPC is a 4-point model and TIP3P is a 3-point model... this ends up
> building a 3-point water model with a mixture of OPC and TIP3P parameters,
> which is *not good*. IIRC you end up with OPC LJ parameters, but TIP3P
> partial charges. so you want to make sure you always load the library that
> matches the water box you assign.
>
>>
>> Thank you again !
>>
>> Enrico
>>
>> Il giorno lun 22 apr 2024 alle ore 17:05 Carlos Simmerling <
>> carlos.simmerling.stonybrook.edu> ha scritto:
>>
>>> indeed, if you look at that structure it is clearly missing an atom from
>>> that phosphate. Others may know why people model structures this way.
>>> I think you need to decide if you want to remove the extra atoms (P,
>>> OP1, OP2), or if you want to build in the missing O. Unfortunately since
>>> the entire OHE is missing, there isn't an easy way to tell
>>> leap it is present if you don't have any coordinates, so leap won't add it
>>> for you. Tools like CHimera allow you to draw in extra atoms quite easily.
>>> there is lots of prior discussion in the archives, look for 5'
>>> phosphate, or "OHE".
>>>
>>>
>>>
>>> On Mon, Apr 22, 2024 at 10:56 AM Enrico Martinez <jmsstarlight.gmail.com>
>>> wrote:
>>>
>>>> Hey, thank you very much for these suggestions !
>>>>
>>>> Actually, I've just tested this on another DNA extracted directly from
>>>> this complex:
>>>>
>>>> https://www.rcsb.org/structure/5FKW
>>>>
>>>> However, I have very similar error
>>>>
>>>> FATAL: Atom .R<DG5 733>.A<P 32> does not have a type.
>>>> FATAL: Atom .R<DG5 733>.A<OP1 33> does not have a type.
>>>> FATAL: Atom .R<DG5 733>.A<OP2 34> does not have a type.
>>>> FATAL: Atom .R<DG5 758>.A<P 32> does not have a type.
>>>> FATAL: Atom .R<DG5 758>.A<OP1 33> does not have a type.
>>>> FATAL: Atom .R<DG5 758>.A<OP2 34> does not have a type.
>>>>
>>>> So what should I do exactly with this structure to parametrize it
>>>> properly ? which part of the DNA (and which chain) should be modified ??
>>>>
>>>> Thank you in advance !
>>>>
>>>> Enrico
>>>>
>>>> Il giorno lun 22 apr 2024 alle ore 16:44 Carlos Simmerling <
>>>> carlos.simmerling.stonybrook.edu> ha scritto:
>>>>
>>>>> your first chain appears to have a 5' phosphate, but is missing one of
>>>>> the oxygen atoms. By default the 5' residues do not include a
>>>>> phosphate. If the oxygen were present you could rename the residue to OHE
>>>>> (giving a different residue number than the DC2). You could also delete
>>>>> the extra atoms so leap doesn't complain. It depends on the source of this
>>>>> structure and what you want to model.
>>>>>
>>>>> however I see another issue in your file - you are loading the OPC
>>>>> water library, but then load the TIP3PBOX. This may not generate an error
>>>>> but is almost certainly not what you want to do. Make sure you haven't done
>>>>> this in any other simulations. Either load the tip3p leaprc, or the
>>>>> OPCBOX.
>>>>>
>>>>>
>>>>> On Mon, Apr 22, 2024 at 10:30 AM Enrico Martinez via AMBER <
>>>>> amber.ambermd.org> wrote:
>>>>>
>>>>>> Dear Amber Users !
>>>>>>
>>>>>> I am trying to parametrize the DNA duplex from the PDB structure,
>>>>>> givven in
>>>>>> the following format:
>>>>>> ATOM 1 P DC C 2 0.997 17.702 5.368 1.00 77.21
>>>>>> A
>>>>>> P
>>>>>> ATOM 2 OP1 DC C 2 -0.278 17.623 4.612 1.00 76.82
>>>>>> A
>>>>>> O
>>>>>> ATOM 3 OP2 DC C 2 1.374 16.596 6.287 1.00 76.77
>>>>>> A
>>>>>> O
>>>>>> ATOM 4 O5' DC C 2 2.181 17.899 4.319 1.00 75.66
>>>>>> A
>>>>>> O
>>>>>> ATOM 5 C5' DC C 2 2.302 19.107 3.565 1.00 72.46
>>>>>> A
>>>>>> C
>>>>>> ATOM 6 C4' DC C 2 2.984 18.826 2.246 1.00 69.77
>>>>>> A
>>>>>> C
>>>>>> ATOM 7 O4' DC C 2 4.361 18.445 2.497 1.00 69.77
>>>>>> A
>>>>>> O
>>>>>> ATOM 8 C3' DC C 2 2.353 17.665 1.476 1.00 67.80
>>>>>> A
>>>>>> C
>>>>>> ATOM 9 O3' DC C 2 2.322 17.915 0.072 1.00 64.34
>>>>>> A
>>>>>> O
>>>>>> ATOM 10 C2' DC C 2 3.282 16.503 1.754 1.00 68.57
>>>>>> A
>>>>>> C
>>>>>> ATOM 11 C1' DC C 2 4.629 17.185 1.899 1.00 69.34
>>>>>> A
>>>>>> C
>>>>>> ATOM 12 N1 DC C 2 5.524 16.432 2.787 1.00 68.89
>>>>>> A
>>>>>> N
>>>>>> ATOM 13 C2 DC C 2 6.729 15.934 2.273 1.00 68.82
>>>>>> A
>>>>>> C
>>>>>> ATOM 14 O2 DC C 2 7.050 16.216 1.107 1.00 69.02
>>>>>> A
>>>>>> O
>>>>>> ATOM 15 N3 DC C 2 7.511 15.163 3.063 1.00 68.41
>>>>>> A
>>>>>> N
>>>>>> ATOM 16 C4 DC C 2 7.137 14.898 4.317 1.00 67.73
>>>>>> A
>>>>>> C
>>>>>> ATOM 17 N4 DC C 2 7.922 14.108 5.051 1.00 68.11
>>>>>> A
>>>>>> N
>>>>>> ATOM 18 C5 DC C 2 5.938 15.427 4.875 1.00 67.80
>>>>>> A
>>>>>> C
>>>>>> ATOM 19 C6 DC C 2 5.172 16.185 4.084 1.00 67.90
>>>>>> A
>>>>>> C
>>>>>> ATOM 20 P DC C 3 1.698 16.807 -0.911 1.00 62.48
>>>>>> A
>>>>>> P
>>>>>> ATOM 21 OP1 DC C 3 0.932 17.528 -1.961 1.00 61.28
>>>>>> A
>>>>>> O
>>>>>> ATOM 22 OP2 DC C 3 1.021 15.775 -0.082 1.00 60.28
>>>>>> A
>>>>>> O
>>>>>> ATOM 23 O5' DC C 3 2.974 16.129 -1.583 1.00 62.05
>>>>>> A
>>>>>> O
>>>>>> ATOM 24 C5' DC C 3 3.892 16.899 -2.357 1.00 61.04
>>>>>> A
>>>>>> C
>>>>>> ATOM 25 C4' DC C 3 4.862 15.986 -3.070 1.00 60.79
>>>>>> A
>>>>>> C
>>>>>> ATOM 26 O4' DC C 3 5.754 15.378 -2.105 1.00 59.07
>>>>>> A
>>>>>> O
>>>>>> ATOM 27 C3' DC C 3 4.190 14.834 -3.814 1.00 61.78
>>>>>> A
>>>>>> C
>>>>>> ATOM 28 O3' DC C 3 4.839 14.587 -5.061 1.00 64.07
>>>>>> A
>>>>>> O
>>>>>> ATOM 29 C2' DC C 3 4.361 13.654 -2.876 1.00 60.89
>>>>>> A
>>>>>> C
>>>>>> ATOM 30 C1' DC C 3 5.674 13.963 -2.180 1.00 58.84
>>>>>> A
>>>>>> C
>>>>>> ATOM 31 N1 DC C 3 5.746 13.432 -0.810 1.00 57.14
>>>>>> A
>>>>>> N
>>>>>> ATOM 32 C2 DC C 3 6.837 12.637 -0.446 1.00 56.58
>>>>>> A
>>>>>> C
>>>>>> ATOM 33 O2 DC C 3 7.733 12.425 -1.279 1.00 56.01
>>>>>> A
>>>>>> O
>>>>>> ATOM 34 N3 DC C 3 6.890 12.121 0.804 1.00 56.47
>>>>>> A
>>>>>> N
>>>>>> ATOM 35 C4 DC C 3 5.910 12.377 1.674 1.00 55.75
>>>>>> A
>>>>>> C
>>>>>> ATOM 36 N4 DC C 3 5.997 11.837 2.892 1.00 54.42
>>>>>> A
>>>>>> N
>>>>>> ATOM 37 C5 DC C 3 4.797 13.196 1.334 1.00 55.79
>>>>>> A
>>>>>> C
>>>>>> ATOM 38 C6 DC C 3 4.756 13.699 0.094 1.00 56.37
>>>>>> A
>>>>>> C
>>>>>> ATOM 39 P DC C 4 4.456 13.276 -5.907 1.00 66.34
>>>>>> A
>>>>>> P
>>>>>> ATOM 40 OP1 DC C 4 4.807 13.537 -7.327 1.00 66.39
>>>>>> A
>>>>>> O
>>>>>> ATOM 41 OP2 DC C 4 3.072 12.869 -5.556 1.00 65.69
>>>>>> A
>>>>>> O
>>>>>> ATOM 42 O5' DC C 4 5.460 12.179 -5.342 1.00 66.82
>>>>>> A
>>>>>> O
>>>>>> ATOM 43 C5' DC C 4 6.857 12.283 -5.602 1.00 67.49
>>>>>> A
>>>>>> C
>>>>>> ATOM 44 C4' DC C 4 7.470 10.907 -5.682 1.00 67.43
>>>>>> A
>>>>>> C
>>>>>> ATOM 45 O4' DC C 4 7.741 10.403 -4.351 1.00 67.85
>>>>>> A
>>>>>> O
>>>>>> ATOM 46 C3' DC C 4 6.554 9.886 -6.353 1.00 68.11
>>>>>> A
>>>>>> C
>>>>>> ATOM 47 O3' DC C 4 7.295 9.054 -7.241 1.00 68.64
>>>>>> A
>>>>>> O
>>>>>> ATOM 48 C2' DC C 4 5.997 9.084 -5.190 1.00 67.75
>>>>>> A
>>>>>> C
>>>>>> ATOM 49 C1' DC C 4 7.129 9.136 -4.177 1.00 67.64
>>>>>> A
>>>>>> C
>>>>>> ATOM 50 N1 DC C 4 6.691 9.032 -2.775 1.00 66.63
>>>>>> A
>>>>>> N
>>>>>> ATOM 51 C2 DC C 4 7.418 8.217 -1.897 1.00 66.70
>>>>>> A
>>>>>> C
>>>>>> ATOM 52 O2 DC C 4 8.421 7.619 -2.320 1.00 66.66
>>>>>> A
>>>>>> O
>>>>>> ATOM 53 N3 DC C 4 7.011 8.104 -0.612 1.00 66.43
>>>>>> A
>>>>>> N
>>>>>> ATOM 54 C4 DC C 4 5.931 8.767 -0.193 1.00 65.41
>>>>>> A
>>>>>> C
>>>>>> ATOM 55 N4 DC C 4 5.563 8.620 1.082 1.00 65.71
>>>>>> A
>>>>>> N
>>>>>> ATOM 56 C5 DC C 4 5.178 9.608 -1.063 1.00 65.35
>>>>>> A
>>>>>> C
>>>>>> ATOM 57 C6 DC C 4 5.590 9.711 -2.333 1.00 65.66
>>>>>> A
>>>>>> C
>>>>>> ATOM 58 P DA C 5 6.540 7.897 -8.054 1.00 69.43
>>>>>> A
>>>>>> P
>>>>>> ATOM 59 OP1 DA C 5 6.970 7.980 -9.475 1.00 70.04
>>>>>> A
>>>>>> O
>>>>>> ATOM 60 OP2 DA C 5 5.094 7.951 -7.718 1.00 69.63
>>>>>> A
>>>>>> O
>>>>>> ATOM 61 O5' DA C 5 7.154 6.572 -7.431 1.00 69.91
>>>>>> A
>>>>>> O
>>>>>> ATOM 62 C5' DA C 5 8.564 6.403 -7.349 1.00 71.69
>>>>>> A
>>>>>> C
>>>>>> ATOM 63 C4' DA C 5 8.886 5.102 -6.657 1.00 73.39
>>>>>> A
>>>>>> C
>>>>>> ATOM 64 O4' DA C 5 8.581 5.216 -5.245 1.00 72.72
>>>>>> A
>>>>>> O
>>>>>> ATOM 65 C3' DA C 5 8.062 3.929 -7.181 1.00 74.71
>>>>>> A
>>>>>> C
>>>>>> ATOM 66 O3' DA C 5 8.866 2.756 -7.266 1.00 78.00
>>>>>> A
>>>>>> O
>>>>>> ATOM 67 C2' DA C 5 6.970 3.767 -6.139 1.00 73.46
>>>>>> A
>>>>>> C
>>>>>> ATOM 68 C1' DA C 5 7.661 4.207 -4.861 1.00 72.08
>>>>>> A
>>>>>> C
>>>>>> ATOM 69 N9 DA C 5 6.753 4.779 -3.865 1.00 70.55
>>>>>> A
>>>>>> N
>>>>>> ATOM 70 C8 DA C 5 5.785 5.734 -4.059 1.00 69.93
>>>>>> A
>>>>>> C
>>>>>> ATOM 71 N7 DA C 5 5.111 6.031 -2.975 1.00 68.91
>>>>>> A
>>>>>> N
>>>>>> ATOM 72 C5 DA C 5 5.674 5.220 -2.000 1.00 68.29
>>>>>> A
>>>>>> C
>>>>>> ATOM 73 C6 DA C 5 5.399 5.057 -0.631 1.00 67.19
>>>>>> A
>>>>>> C
>>>>>> ATOM 74 N6 DA C 5 4.443 5.725 0.016 1.00 66.51
>>>>>> A
>>>>>> N
>>>>>> ATOM 75 N1 DA C 5 6.147 4.169 0.059 1.00 67.29
>>>>>> A
>>>>>> N
>>>>>> ATOM 76 C2 DA C 5 7.103 3.494 -0.593 1.00 68.25
>>>>>> A
>>>>>> C
>>>>>> ATOM 77 N3 DA C 5 7.454 3.557 -1.876 1.00 68.56
>>>>>> A
>>>>>> N
>>>>>> ATOM 78 C4 DA C 5 6.692 4.449 -2.532 1.00 69.05
>>>>>> A
>>>>>> C
>>>>>> ATOM 79 P DT C 6 8.222 1.391 -7.808 1.00 81.00
>>>>>> A
>>>>>> P
>>>>>> ATOM 80 OP1 DT C 6 9.158 0.830 -8.815 1.00 81.11
>>>>>> A
>>>>>> O
>>>>>> ATOM 81 OP2 DT C 6 6.807 1.650 -8.183 1.00 80.85
>>>>>> A
>>>>>> O
>>>>>> ATOM 82 O5' DT C 6 8.242 0.456 -6.520 1.00 82.33
>>>>>> A
>>>>>> O
>>>>>> ATOM 83 C5' DT C 6 9.365 0.463 -5.642 1.00 85.09
>>>>>> A
>>>>>> C
>>>>>> ATOM 84 C4' DT C 6 9.006 -0.177 -4.321 1.00 87.48
>>>>>> A
>>>>>> C
>>>>>> ATOM 85 O4' DT C 6 8.089 0.669 -3.581 1.00 87.16
>>>>>> A
>>>>>> O
>>>>>> ATOM 86 C3' DT C 6 8.322 -1.539 -4.439 1.00 89.51
>>>>>> A
>>>>>> C
>>>>>> ATOM 87 O3' DT C 6 8.822 -2.418 -3.424 1.00 93.36
>>>>>> A
>>>>>> O
>>>>>> ATOM 88 C2' DT C 6 6.858 -1.217 -4.193 1.00 88.28
>>>>>> A
>>>>>> C
>>>>>> ATOM 89 C1' DT C 6 6.963 -0.098 -3.179 1.00 86.81
>>>>>> A
>>>>>> C
>>>>>> ATOM 90 N1 DT C 6 5.791 0.798 -3.109 1.00 85.59
>>>>>> A
>>>>>> N
>>>>>> ATOM 91 C2 DT C 6 5.212 1.000 -1.876 1.00 85.30
>>>>>> A
>>>>>> C
>>>>>> ATOM 92 O2 DT C 6 5.620 0.471 -0.854 1.00 85.01
>>>>>> A
>>>>>> O
>>>>>> ATOM 93 N3 DT C 6 4.131 1.849 -1.881 1.00 84.88
>>>>>> A
>>>>>> N
>>>>>> ATOM 94 C4 DT C 6 3.584 2.498 -2.972 1.00 84.82
>>>>>> A
>>>>>> C
>>>>>> ATOM 95 O4 DT C 6 2.615 3.238 -2.820 1.00 84.15
>>>>>> A
>>>>>> O
>>>>>> ATOM 96 C5 DT C 6 4.235 2.233 -4.236 1.00 85.05
>>>>>> A
>>>>>> C
>>>>>> ATOM 97 C7 DT C 6 3.704 2.883 -5.475 1.00 84.91
>>>>>> A
>>>>>> C
>>>>>> ATOM 98 C6 DT C 6 5.294 1.409 -4.241 1.00 85.39
>>>>>> A
>>>>>> C
>>>>>> ATOM 99 P DC C 7 7.989 -3.732 -3.028 1.00 95.28
>>>>>> A
>>>>>> P
>>>>>> ATOM 100 OP1 DC C 7 8.883 -4.615 -2.235 1.00 94.63
>>>>>> A
>>>>>> O
>>>>>> ATOM 101 OP2 DC C 7 7.334 -4.259 -4.254 1.00 95.32
>>>>>> A
>>>>>> O
>>>>>> ATOM 102 O5' DC C 7 6.860 -3.170 -2.056 1.00 96.43
>>>>>> A
>>>>>> O
>>>>>> ATOM 103 C5' DC C 7 7.085 -3.086 -0.652 1.00 98.11
>>>>>> A
>>>>>> C
>>>>>> ATOM 104 C4' DC C 7 5.902 -3.660 0.088 1.00 99.34
>>>>>> A
>>>>>> C
>>>>>> ATOM 105 O4' DC C 7 4.811 -2.708 0.083 1.00 99.36
>>>>>> A
>>>>>> O
>>>>>> ATOM 106 C3' DC C 7 5.362 -4.934 -0.561 1.00100.54
>>>>>> A
>>>>>> C
>>>>>> ATOM 107 O3' DC C 7 4.969 -5.879 0.436 1.00102.51
>>>>>> A
>>>>>> O
>>>>>> ATOM 108 C2' DC C 7 4.165 -4.445 -1.356 1.00100.01
>>>>>> A
>>>>>> C
>>>>>> ATOM 109 C1' DC C 7 3.659 -3.288 -0.509 1.00 99.10
>>>>>> A
>>>>>> C
>>>>>> ATOM 110 N1 DC C 7 2.950 -2.229 -1.249 1.00 98.13
>>>>>> A
>>>>>> N
>>>>>> ATOM 111 C2 DC C 7 2.251 -1.257 -0.524 1.00 97.59
>>>>>> A
>>>>>> C
>>>>>> ATOM 112 O2 DC C 7 2.257 -1.315 0.715 1.00 97.25
>>>>>> A
>>>>>> O
>>>>>> ATOM 113 N3 DC C 7 1.590 -0.282 -1.188 1.00 97.12
>>>>>> A
>>>>>> N
>>>>>> ATOM 114 C4 DC C 7 1.610 -0.253 -2.522 1.00 97.24
>>>>>> A
>>>>>> C
>>>>>> ATOM 115 N4 DC C 7 0.942 0.727 -3.135 1.00 96.86
>>>>>> A
>>>>>> N
>>>>>> ATOM 116 C5 DC C 7 2.316 -1.227 -3.287 1.00 97.43
>>>>>> A
>>>>>> C
>>>>>> ATOM 117 C6 DC C 7 2.967 -2.188 -2.617 1.00 97.80
>>>>>> A
>>>>>> C
>>>>>> ATOM 118 P DG C 8 5.512 -7.389 0.354 1.00103.68
>>>>>> A
>>>>>> P
>>>>>> ATOM 119 OP1 DG C 8 6.964 -7.363 0.671 1.00103.46
>>>>>> A
>>>>>> O
>>>>>> ATOM 120 OP2 DG C 8 5.050 -7.989 -0.925 1.00103.69
>>>>>> A
>>>>>> O
>>>>>> ATOM 121 O5' DG C 8 4.763 -8.122 1.549 1.00103.36
>>>>>> A
>>>>>> O
>>>>>> ATOM 122 C5' DG C 8 4.938 -7.690 2.895 1.00102.90
>>>>>> A
>>>>>> C
>>>>>> ATOM 123 C4' DG C 8 3.609 -7.688 3.610 1.00102.30
>>>>>> A
>>>>>> C
>>>>>> ATOM 124 O4' DG C 8 2.800 -6.588 3.122 1.00101.30
>>>>>> A
>>>>>> O
>>>>>> ATOM 125 C3' DG C 8 2.789 -8.957 3.375 1.00102.54
>>>>>> A
>>>>>> C
>>>>>> ATOM 126 O3' DG C 8 2.123 -9.361 4.574 1.00103.80
>>>>>> A
>>>>>> O
>>>>>> ATOM 127 C2' DG C 8 1.789 -8.539 2.312 1.00101.61
>>>>>> A
>>>>>> C
>>>>>> ATOM 128 C1' DG C 8 1.556 -7.075 2.640 1.00100.21
>>>>>> A
>>>>>> C
>>>>>> ATOM 129 N9 DG C 8 1.162 -6.259 1.494 1.00 98.16
>>>>>> A
>>>>>> N
>>>>>> ATOM 130 C8 DG C 8 1.663 -6.331 0.216 1.00 97.31
>>>>>> A
>>>>>> C
>>>>>> ATOM 131 N7 DG C 8 1.107 -5.478 -0.601 1.00 96.55
>>>>>> A
>>>>>> N
>>>>>> ATOM 132 C5 DG C 8 0.185 -4.799 0.184 1.00 96.28
>>>>>> A
>>>>>> C
>>>>>> ATOM 133 C6 DG C 8 -0.718 -3.754 -0.152 1.00 95.76
>>>>>> A
>>>>>> C
>>>>>> ATOM 134 O6 DG C 8 -0.888 -3.204 -1.247 1.00 94.96
>>>>>> A
>>>>>> O
>>>>>> ATOM 135 N1 DG C 8 -1.472 -3.356 0.947 1.00 95.55
>>>>>> A
>>>>>> N
>>>>>> ATOM 136 C2 DG C 8 -1.373 -3.891 2.208 1.00 95.99
>>>>>> A
>>>>>> C
>>>>>> ATOM 137 N2 DG C 8 -2.188 -3.368 3.136 1.00 95.83
>>>>>> A
>>>>>> N
>>>>>> ATOM 138 N3 DG C 8 -0.536 -4.865 2.535 1.00 96.52
>>>>>> A
>>>>>> N
>>>>>> ATOM 139 C4 DG C 8 0.207 -5.268 1.481 1.00 96.99
>>>>>> A
>>>>>> C
>>>>>> ATOM 140 P DT C 9 1.062 -10.567 4.525 1.00105.08
>>>>>> A
>>>>>> P
>>>>>> ATOM 141 OP1 DT C 9 0.907 -11.084 5.908 1.00105.25
>>>>>> A
>>>>>> O
>>>>>> ATOM 142 OP2 DT C 9 1.453 -11.496 3.435 1.00105.09
>>>>>> A
>>>>>> O
>>>>>> ATOM 143 O5' DT C 9 -0.292 -9.843 4.101 1.00106.04
>>>>>> A
>>>>>> O
>>>>>> ATOM 144 C5' DT C 9 -0.719 -8.656 4.772 1.00107.19
>>>>>> A
>>>>>> C
>>>>>> ATOM 145 C4' DT C 9 -1.980 -8.116 4.138 1.00107.81
>>>>>> A
>>>>>> C
>>>>>> ATOM 146 O4' DT C 9 -1.690 -7.559 2.833 1.00107.68
>>>>>> A
>>>>>> O
>>>>>> ATOM 147 C3' DT C 9 -3.078 -9.157 3.923 1.00108.50
>>>>>> A
>>>>>> C
>>>>>> ATOM 148 O3' DT C 9 -4.354 -8.573 4.194 1.00109.70
>>>>>> A
>>>>>> O
>>>>>> ATOM 149 C2' DT C 9 -2.962 -9.479 2.444 1.00107.93
>>>>>> A
>>>>>> C
>>>>>> ATOM 150 C1' DT C 9 -2.564 -8.131 1.873 1.00107.38
>>>>>> A
>>>>>> C
>>>>>> ATOM 151 N1 DT C 9 -1.857 -8.182 0.580 1.00106.81
>>>>>> A
>>>>>> N
>>>>>> ATOM 152 C2 DT C 9 -2.250 -7.300 -0.402 1.00106.50
>>>>>> A
>>>>>> C
>>>>>> ATOM 153 O2 DT C 9 -3.139 -6.479 -0.244 1.00105.95
>>>>>> A
>>>>>> O
>>>>>> ATOM 154 N3 DT C 9 -1.560 -7.413 -1.583 1.00106.39
>>>>>> A
>>>>>> N
>>>>>> ATOM 155 C4 DT C 9 -0.537 -8.297 -1.872 1.00106.47
>>>>>> A
>>>>>> C
>>>>>> ATOM 156 O4 DT C 9 -0.015 -8.285 -2.983 1.00106.12
>>>>>> A
>>>>>> O
>>>>>> ATOM 157 C5 DT C 9 -0.169 -9.187 -0.792 1.00106.52
>>>>>> A
>>>>>> C
>>>>>> ATOM 158 C7 DT C 9 0.936 -10.172 -1.007 1.00106.19
>>>>>> A
>>>>>> C
>>>>>> ATOM 159 C6 DT C 9 -0.840 -9.086 0.363 1.00106.63
>>>>>> A
>>>>>> C
>>>>>> ATOM 160 P DA C 10 -5.368 -9.305 5.202 1.00110.59
>>>>>> A
>>>>>> P
>>>>>> ATOM 161 OP1 DA C 10 -4.805 -9.175 6.571 1.00110.18
>>>>>> A
>>>>>> O
>>>>>> ATOM 162 OP2 DA C 10 -5.672 -10.655 4.657 1.00110.16
>>>>>> A
>>>>>> O
>>>>>> ATOM 163 O5' DA C 10 -6.688 -8.417 5.119 1.00110.49
>>>>>> A
>>>>>> O
>>>>>> ATOM 164 C5' DA C 10 -6.658 -7.026 5.441 1.00110.26
>>>>>> A
>>>>>> C
>>>>>> ATOM 165 C4' DA C 10 -7.425 -6.237 4.406 1.00110.22
>>>>>> A
>>>>>> C
>>>>>> ATOM 166 O4' DA C 10 -6.728 -6.307 3.137 1.00109.62
>>>>>> A
>>>>>> O
>>>>>> ATOM 167 C3' DA C 10 -8.837 -6.757 4.137 1.00110.54
>>>>>> A
>>>>>> C
>>>>>> ATOM 168 O3' DA C 10 -9.726 -5.670 3.866 1.00111.83
>>>>>> A
>>>>>> O
>>>>>> ATOM 169 C2' DA C 10 -8.663 -7.609 2.895 1.00109.75
>>>>>> A
>>>>>> C
>>>>>> ATOM 170 C1' DA C 10 -7.584 -6.854 2.143 1.00108.67
>>>>>> A
>>>>>> C
>>>>>> ATOM 171 N9 DA C 10 -6.774 -7.696 1.264 1.00107.35
>>>>>> A
>>>>>> N
>>>>>> ATOM 172 C8 DA C 10 -6.143 -8.876 1.573 1.00106.77
>>>>>> A
>>>>>> C
>>>>>> ATOM 173 N7 DA C 10 -5.490 -9.405 0.568 1.00106.24
>>>>>> A
>>>>>> N
>>>>>> ATOM 174 C5 DA C 10 -5.705 -8.514 -0.474 1.00106.32
>>>>>> A
>>>>>> C
>>>>>> ATOM 175 C6 DA C 10 -5.277 -8.504 -1.814 1.00106.15
>>>>>> A
>>>>>> C
>>>>>> ATOM 176 N6 DA C 10 -4.511 -9.454 -2.355 1.00105.78
>>>>>> A
>>>>>> N
>>>>>> ATOM 177 N1 DA C 10 -5.669 -7.470 -2.589 1.00106.16
>>>>>> A
>>>>>> N
>>>>>> ATOM 178 C2 DA C 10 -6.437 -6.516 -2.046 1.00106.34
>>>>>> A
>>>>>> C
>>>>>> ATOM 179 N3 DA C 10 -6.902 -6.415 -0.803 1.00106.32
>>>>>> A
>>>>>> N
>>>>>> ATOM 180 C4 DA C 10 -6.495 -7.457 -0.059 1.00106.58
>>>>>> A
>>>>>> C
>>>>>> ATOM 181 P DT C 11 -11.239 -5.974 3.415 1.00113.08
>>>>>> A
>>>>>> P
>>>>>> ATOM 182 OP1 DT C 11 -12.049 -4.766 3.723 1.00112.97
>>>>>> A
>>>>>> O
>>>>>> ATOM 183 OP2 DT C 11 -11.635 -7.289 3.985 1.00113.19
>>>>>> A
>>>>>> O
>>>>>> ATOM 184 O5' DT C 11 -11.149 -6.121 1.830 1.00112.44
>>>>>> A
>>>>>> O
>>>>>> ATOM 185 C5' DT C 11 -10.880 -4.987 1.004 1.00111.79
>>>>>> A
>>>>>> C
>>>>>> ATOM 186 C4' DT C 11 -11.170 -5.308 -0.445 1.00111.20
>>>>>> A
>>>>>> C
>>>>>> ATOM 187 O4' DT C 11 -10.229 -6.303 -0.916 1.00110.99
>>>>>> A
>>>>>> O
>>>>>> ATOM 188 C3' DT C 11 -12.556 -5.893 -0.713 1.00110.92
>>>>>> A
>>>>>> C
>>>>>> ATOM 189 O3' DT C 11 -12.939 -5.622 -2.063 1.00110.58
>>>>>> A
>>>>>> O
>>>>>> ATOM 190 C2' DT C 11 -12.301 -7.387 -0.653 1.00110.76
>>>>>> A
>>>>>> C
>>>>>> ATOM 191 C1' DT C 11 -10.920 -7.490 -1.285 1.00110.50
>>>>>> A
>>>>>> C
>>>>>> ATOM 192 N1 DT C 11 -10.111 -8.639 -0.835 1.00110.18
>>>>>> A
>>>>>> N
>>>>>> ATOM 193 C2 DT C 11 -9.114 -9.087 -1.670 1.00109.85
>>>>>> A
>>>>>> C
>>>>>> ATOM 194 O2 DT C 11 -8.880 -8.582 -2.755 1.00109.15
>>>>>> A
>>>>>> O
>>>>>> ATOM 195 N3 DT C 11 -8.397 -10.153 -1.185 1.00109.91
>>>>>> A
>>>>>> N
>>>>>> ATOM 196 C4 DT C 11 -8.575 -10.800 0.024 1.00109.98
>>>>>> A
>>>>>> C
>>>>>> ATOM 197 O4 DT C 11 -7.848 -11.744 0.326 1.00109.88
>>>>>> A
>>>>>> O
>>>>>> ATOM 198 C5 DT C 11 -9.643 -10.280 0.850 1.00110.02
>>>>>> A
>>>>>> C
>>>>>> ATOM 199 C7 DT C 11 -9.913 -10.918 2.176 1.00109.72
>>>>>> A
>>>>>> C
>>>>>> ATOM 200 C6 DT C 11 -10.348 -9.240 0.385 1.00110.11
>>>>>> A
>>>>>> C
>>>>>> TER
>>>>>> ATOM 201 O5' DT D 11 -10.392 -20.352 4.929 1.00 76.79
>>>>>> B
>>>>>> O
>>>>>> ATOM 202 C5' DT D 11 -9.896 -21.479 4.202 1.00 77.01
>>>>>> B
>>>>>> C
>>>>>> ATOM 203 C4' DT D 11 -9.795 -21.223 2.715 1.00 77.22
>>>>>> B
>>>>>> C
>>>>>> ATOM 204 O4' DT D 11 -11.117 -21.026 2.158 1.00 76.23
>>>>>> B
>>>>>> O
>>>>>> ATOM 205 C3' DT D 11 -8.985 -19.984 2.334 1.00 77.90
>>>>>> B
>>>>>> C
>>>>>> ATOM 206 O3' DT D 11 -8.251 -20.235 1.131 1.00 80.40
>>>>>> B
>>>>>> O
>>>>>> ATOM 207 C2' DT D 11 -10.054 -18.932 2.093 1.00 76.66
>>>>>> B
>>>>>> C
>>>>>> ATOM 208 C1' DT D 11 -11.202 -19.754 1.529 1.00 74.87
>>>>>> B
>>>>>> C
>>>>>> ATOM 209 N1 DT D 11 -12.542 -19.207 1.812 1.00 72.73
>>>>>> B
>>>>>> N
>>>>>> ATOM 210 C2 DT D 11 -13.242 -18.601 0.790 1.00 71.47
>>>>>> B
>>>>>> C
>>>>>> ATOM 211 O2 DT D 11 -12.805 -18.477 -0.342 1.00 69.73
>>>>>> B
>>>>>> O
>>>>>> ATOM 212 N3 DT D 11 -14.484 -18.141 1.147 1.00 70.82
>>>>>> B
>>>>>> N
>>>>>> ATOM 213 C4 DT D 11 -15.081 -18.223 2.392 1.00 70.41
>>>>>> B
>>>>>> C
>>>>>> ATOM 214 O4 DT D 11 -16.207 -17.769 2.560 1.00 70.78
>>>>>> B
>>>>>> O
>>>>>> ATOM 215 C5 DT D 11 -14.289 -18.862 3.415 1.00 70.87
>>>>>> B
>>>>>> C
>>>>>> ATOM 216 C7 DT D 11 -14.852 -18.993 4.794 1.00 69.83
>>>>>> B
>>>>>> C
>>>>>> ATOM 217 C6 DT D 11 -13.075 -19.314 3.078 1.00 71.79
>>>>>> B
>>>>>> C
>>>>>> ATOM 218 P DT D 12 -6.643 -20.240 1.163 1.00 82.44
>>>>>> B
>>>>>> P
>>>>>> ATOM 219 OP1 DT D 12 -6.216 -21.273 2.144 1.00 81.59
>>>>>> B
>>>>>> O
>>>>>> ATOM 220 OP2 DT D 12 -6.171 -18.839 1.317 1.00 82.43
>>>>>> B
>>>>>> O
>>>>>> ATOM 221 O5' DT D 12 -6.236 -20.743 -0.293 1.00 82.08
>>>>>> B
>>>>>> O
>>>>>> ATOM 222 C5' DT D 12 -4.892 -21.112 -0.595 1.00 82.34
>>>>>> B
>>>>>> C
>>>>>> ATOM 223 C4' DT D 12 -4.604 -20.865 -2.057 1.00 82.27
>>>>>> B
>>>>>> C
>>>>>> ATOM 224 O4' DT D 12 -5.449 -21.724 -2.859 1.00 81.43
>>>>>> B
>>>>>> O
>>>>>> ATOM 225 C3' DT D 12 -4.905 -19.439 -2.511 1.00 82.71
>>>>>> B
>>>>>> C
>>>>>> ATOM 226 O3' DT D 12 -3.965 -19.023 -3.503 1.00 84.47
>>>>>> B
>>>>>> O
>>>>>> ATOM 227 C2' DT D 12 -6.304 -19.537 -3.089 1.00 81.53
>>>>>> B
>>>>>> C
>>>>>> ATOM 228 C1' DT D 12 -6.352 -20.953 -3.643 1.00 80.15
>>>>>> B
>>>>>> C
>>>>>> ATOM 229 N1 DT D 12 -7.682 -21.577 -3.524 1.00 78.17
>>>>>> B
>>>>>> N
>>>>>> ATOM 230 C2 DT D 12 -8.352 -21.936 -4.672 1.00 77.20
>>>>>> B
>>>>>> C
>>>>>> ATOM 231 O2 DT D 12 -7.901 -21.760 -5.792 1.00 76.81
>>>>>> B
>>>>>> O
>>>>>> ATOM 232 N3 DT D 12 -9.580 -22.511 -4.457 1.00 76.03
>>>>>> B
>>>>>> N
>>>>>> ATOM 233 C4 DT D 12 -10.187 -22.754 -3.239 1.00 76.02
>>>>>> B
>>>>>> C
>>>>>> ATOM 234 O4 DT D 12 -11.292 -23.280 -3.201 1.00 76.05
>>>>>> B
>>>>>> O
>>>>>> ATOM 235 C5 DT D 12 -9.428 -22.350 -2.081 1.00 76.49
>>>>>> B
>>>>>> C
>>>>>> ATOM 236 C7 DT D 12 -10.008 -22.569 -0.719 1.00 75.76
>>>>>> B
>>>>>> C
>>>>>> ATOM 237 C6 DT D 12 -8.230 -21.791 -2.279 1.00 77.05
>>>>>> B
>>>>>> C
>>>>>> ATOM 238 P DT D 13 -3.741 -17.457 -3.773 1.00 85.69
>>>>>> B
>>>>>> P
>>>>>> ATOM 239 OP1 DT D 13 -2.309 -17.262 -4.118 1.00 85.60
>>>>>> B
>>>>>> O
>>>>>> ATOM 240 OP2 DT D 13 -4.335 -16.699 -2.641 1.00 85.62
>>>>>> B
>>>>>> O
>>>>>> ATOM 241 O5' DT D 13 -4.612 -17.169 -5.074 1.00 85.46
>>>>>> B
>>>>>> O
>>>>>> ATOM 242 C5' DT D 13 -4.002 -17.099 -6.359 1.00 85.44
>>>>>> B
>>>>>> C
>>>>>> ATOM 243 C4' DT D 13 -4.874 -16.305 -7.302 1.00 85.46
>>>>>> B
>>>>>> C
>>>>>> ATOM 244 O4' DT D 13 -6.053 -17.070 -7.648 1.00 84.32
>>>>>> B
>>>>>> O
>>>>>> ATOM 245 C3' DT D 13 -5.384 -14.985 -6.718 1.00 86.35
>>>>>> B
>>>>>> C
>>>>>> ATOM 246 O3' DT D 13 -5.482 -14.014 -7.756 1.00 88.98
>>>>>> B
>>>>>> O
>>>>>> ATOM 247 C2' DT D 13 -6.791 -15.335 -6.274 1.00 84.90
>>>>>> B
>>>>>> C
>>>>>> ATOM 248 C1' DT D 13 -7.204 -16.290 -7.378 1.00 82.93
>>>>>> B
>>>>>> C
>>>>>> ATOM 249 N1 DT D 13 -8.306 -17.201 -7.040 1.00 80.47
>>>>>> B
>>>>>> N
>>>>>> ATOM 250 C2 DT D 13 -9.148 -17.587 -8.055 1.00 78.98
>>>>>> B
>>>>>> C
>>>>>> ATOM 251 O2 DT D 13 -9.008 -17.225 -9.212 1.00 76.66
>>>>>> B
>>>>>> O
>>>>>> ATOM 252 N3 DT D 13 -10.167 -18.418 -7.665 1.00 78.58
>>>>>> B
>>>>>> N
>>>>>> ATOM 253 C4 DT D 13 -10.418 -18.890 -6.390 1.00 78.54
>>>>>> B
>>>>>> C
>>>>>> ATOM 254 O4 DT D 13 -11.376 -19.625 -6.192 1.00 77.80
>>>>>> B
>>>>>> O
>>>>>> ATOM 255 C5 DT D 13 -9.487 -18.450 -5.375 1.00 78.99
>>>>>> B
>>>>>> C
>>>>>> ATOM 256 C7 DT D 13 -9.677 -18.910 -3.964 1.00 78.47
>>>>>> B
>>>>>> C
>>>>>> ATOM 257 C6 DT D 13 -8.490 -17.641 -5.747 1.00 79.90
>>>>>> B
>>>>>> C
>>>>>> ATOM 258 P DT D 14 -4.223 -13.090 -8.109 1.00 90.58
>>>>>> B
>>>>>> P
>>>>>> ATOM 259 OP1 DT D 14 -3.004 -13.933 -8.003 1.00 90.96
>>>>>> B
>>>>>> O
>>>>>> ATOM 260 OP2 DT D 14 -4.320 -11.833 -7.322 1.00 90.93
>>>>>> B
>>>>>> O
>>>>>> ATOM 261 O5' DT D 14 -4.472 -12.753 -9.643 1.00 90.96
>>>>>> B
>>>>>> O
>>>>>> ATOM 262 C5' DT D 14 -5.177 -13.676 -10.472 1.00 91.47
>>>>>> B
>>>>>> C
>>>>>> ATOM 263 C4' DT D 14 -6.395 -13.015 -11.074 1.00 91.65
>>>>>> B
>>>>>> C
>>>>>> ATOM 264 O4' DT D 14 -7.303 -12.613 -10.018 1.00 91.63
>>>>>> B
>>>>>> O
>>>>>> ATOM 265 C3' DT D 14 -6.083 -11.746 -11.866 1.00 91.86
>>>>>> B
>>>>>> C
>>>>>> ATOM 266 O3' DT D 14 -6.936 -11.662 -13.011 1.00 91.50
>>>>>> B
>>>>>> O
>>>>>> ATOM 267 C2' DT D 14 -6.402 -10.635 -10.883 1.00 91.37
>>>>>> B
>>>>>> C
>>>>>> ATOM 268 C1' DT D 14 -7.568 -11.220 -10.114 1.00 91.14
>>>>>> B
>>>>>> C
>>>>>> ATOM 269 N1 DT D 14 -7.708 -10.680 -8.750 1.00 90.43
>>>>>> B
>>>>>> N
>>>>>> ATOM 270 C2 DT D 14 -8.306 -9.449 -8.609 1.00 90.15
>>>>>> B
>>>>>> C
>>>>>> ATOM 271 O2 DT D 14 -8.734 -8.804 -9.552 1.00 89.88
>>>>>> B
>>>>>> O
>>>>>> ATOM 272 N3 DT D 14 -8.385 -8.998 -7.315 1.00 89.91
>>>>>> B
>>>>>> N
>>>>>> ATOM 273 C4 DT D 14 -7.939 -9.641 -6.177 1.00 89.91
>>>>>> B
>>>>>> C
>>>>>> ATOM 274 O4 DT D 14 -8.071 -9.105 -5.081 1.00 90.07
>>>>>> B
>>>>>> O
>>>>>> ATOM 275 C5 DT D 14 -7.333 -10.935 -6.398 1.00 89.91
>>>>>> B
>>>>>> C
>>>>>> ATOM 276 C7 DT D 14 -6.830 -11.712 -5.223 1.00 89.25
>>>>>> B
>>>>>> C
>>>>>> ATOM 277 C6 DT D 14 -7.249 -11.383 -7.657 1.00 90.06
>>>>>> B
>>>>>> C
>>>>>> ATOM 278 P DA D 15 -6.296 -11.402 -14.461 1.00 91.71
>>>>>> B
>>>>>> P
>>>>>> ATOM 279 OP1 DA D 15 -7.380 -11.595 -15.457 1.00 91.72
>>>>>> B
>>>>>> O
>>>>>> ATOM 280 OP2 DA D 15 -5.045 -12.199 -14.569 1.00 91.49
>>>>>> B
>>>>>> O
>>>>>> ATOM 281 O5' DA D 15 -5.904 -9.859 -14.446 1.00 90.66
>>>>>> B
>>>>>> O
>>>>>> ATOM 282 C5' DA D 15 -6.491 -8.976 -13.501 1.00 89.03
>>>>>> B
>>>>>> C
>>>>>> ATOM 283 C4' DA D 15 -7.097 -7.783 -14.197 1.00 88.22
>>>>>> B
>>>>>> C
>>>>>> ATOM 284 O4' DA D 15 -7.953 -8.225 -15.277 1.00 88.02
>>>>>> B
>>>>>> O
>>>>>> ATOM 285 C3' DA D 15 -7.978 -6.949 -13.274 1.00 87.92
>>>>>> B
>>>>>> C
>>>>>> ATOM 286 O3' DA D 15 -7.820 -5.562 -13.560 1.00 88.16
>>>>>> B
>>>>>> O
>>>>>> ATOM 287 C2' DA D 15 -9.383 -7.423 -13.594 1.00 87.92
>>>>>> B
>>>>>> C
>>>>>> ATOM 288 C1' DA D 15 -9.287 -7.784 -15.065 1.00 87.43
>>>>>> B
>>>>>> C
>>>>>> ATOM 289 N9 DA D 15 -10.182 -8.867 -15.473 1.00 87.21
>>>>>> B
>>>>>> N
>>>>>> ATOM 290 C8 DA D 15 -9.833 -10.090 -15.991 1.00 86.99
>>>>>> B
>>>>>> C
>>>>>> ATOM 291 N7 DA D 15 -10.858 -10.859 -16.270 1.00 86.50
>>>>>> B
>>>>>> N
>>>>>> ATOM 292 C5 DA D 15 -11.956 -10.091 -15.911 1.00 86.46
>>>>>> B
>>>>>> C
>>>>>> ATOM 293 C6 DA D 15 -13.338 -10.339 -15.962 1.00 86.32
>>>>>> B
>>>>>> C
>>>>>> ATOM 294 N6 DA D 15 -13.869 -11.478 -16.414 1.00 86.08
>>>>>> B
>>>>>> N
>>>>>> ATOM 295 N1 DA D 15 -14.167 -9.365 -15.527 1.00 86.17
>>>>>> B
>>>>>> N
>>>>>> ATOM 296 C2 DA D 15 -13.632 -8.224 -15.073 1.00 86.59
>>>>>> B
>>>>>> C
>>>>>> ATOM 297 N3 DA D 15 -12.351 -7.873 -14.975 1.00 86.48
>>>>>> B
>>>>>> N
>>>>>> ATOM 298 C4 DA D 15 -11.555 -8.862 -15.417 1.00 86.76
>>>>>> B
>>>>>> C
>>>>>> ATOM 299 P DT D 16 -6.994 -4.640 -12.540 1.00 88.29
>>>>>> B
>>>>>> P
>>>>>> ATOM 300 OP1 DT D 16 -7.488 -3.248 -12.697 1.00 87.78
>>>>>> B
>>>>>> O
>>>>>> ATOM 301 OP2 DT D 16 -5.551 -4.935 -12.730 1.00 88.18
>>>>>> B
>>>>>> O
>>>>>> ATOM 302 O5' DT D 16 -7.431 -5.176 -11.103 1.00 88.33
>>>>>> B
>>>>>> O
>>>>>> ATOM 303 C5' DT D 16 -8.810 -5.309 -10.760 1.00 88.28
>>>>>> B
>>>>>> C
>>>>>> ATOM 304 C4' DT D 16 -9.073 -4.701 -9.403 1.00 88.29
>>>>>> B
>>>>>> C
>>>>>> ATOM 305 O4' DT D 16 -8.575 -5.566 -8.354 1.00 87.95
>>>>>> B
>>>>>> O
>>>>>> ATOM 306 C3' DT D 16 -8.404 -3.344 -9.190 1.00 88.53
>>>>>> B
>>>>>> C
>>>>>> ATOM 307 O3' DT D 16 -9.285 -2.468 -8.489 1.00 89.63
>>>>>> B
>>>>>> O
>>>>>> ATOM 308 C2' DT D 16 -7.204 -3.675 -8.322 1.00 87.85
>>>>>> B
>>>>>> C
>>>>>> ATOM 309 C1' DT D 16 -7.741 -4.817 -7.483 1.00 87.27
>>>>>> B
>>>>>> C
>>>>>> ATOM 310 N1 DT D 16 -6.716 -5.723 -6.939 1.00 85.97
>>>>>> B
>>>>>> N
>>>>>> ATOM 311 C2 DT D 16 -6.538 -5.746 -5.575 1.00 85.35
>>>>>> B
>>>>>> C
>>>>>> ATOM 312 O2 DT D 16 -7.186 -5.053 -4.808 1.00 84.17
>>>>>> B
>>>>>> O
>>>>>> ATOM 313 N3 DT D 16 -5.569 -6.614 -5.138 1.00 85.24
>>>>>> B
>>>>>> N
>>>>>> ATOM 314 C4 DT D 16 -4.781 -7.444 -5.913 1.00 85.85
>>>>>> B
>>>>>> C
>>>>>> ATOM 315 O4 DT D 16 -3.950 -8.174 -5.377 1.00 85.94
>>>>>> B
>>>>>> O
>>>>>> ATOM 316 C5 DT D 16 -5.022 -7.369 -7.337 1.00 85.81
>>>>>> B
>>>>>> C
>>>>>> ATOM 317 C7 DT D 16 -4.217 -8.233 -8.256 1.00 85.50
>>>>>> B
>>>>>> C
>>>>>> ATOM 318 C6 DT D 16 -5.964 -6.522 -7.773 1.00 85.65
>>>>>> B
>>>>>> C
>>>>>> ATOM 319 P DA D 17 -8.955 -0.899 -8.425 1.00 90.43
>>>>>> B
>>>>>> P
>>>>>> ATOM 320 OP1 DA D 17 -10.170 -0.175 -8.877 1.00 90.41
>>>>>> B
>>>>>> O
>>>>>> ATOM 321 OP2 DA D 17 -7.659 -0.656 -9.107 1.00 89.81
>>>>>> B
>>>>>> O
>>>>>> ATOM 322 O5' DA D 17 -8.755 -0.626 -6.871 1.00 90.53
>>>>>> B
>>>>>> O
>>>>>> ATOM 323 C5' DA D 17 -9.837 -0.781 -5.956 1.00 91.26
>>>>>> B
>>>>>> C
>>>>>> ATOM 324 C4' DA D 17 -9.403 -0.361 -4.572 1.00 91.80
>>>>>> B
>>>>>> C
>>>>>> ATOM 325 O4' DA D 17 -8.472 -1.335 -4.041 1.00 91.37
>>>>>> B
>>>>>> O
>>>>>> ATOM 326 C3' DA D 17 -8.671 0.980 -4.543 1.00 92.51
>>>>>> B
>>>>>> C
>>>>>> ATOM 327 O3' DA D 17 -8.983 1.685 -3.340 1.00 94.52
>>>>>> B
>>>>>> O
>>>>>> ATOM 328 C2' DA D 17 -7.209 0.575 -4.548 1.00 91.45
>>>>>> B
>>>>>> C
>>>>>> ATOM 329 C1' DA D 17 -7.235 -0.708 -3.737 1.00 90.50
>>>>>> B
>>>>>> C
>>>>>> ATOM 330 N9 DA D 17 -6.164 -1.651 -4.059 1.00 89.36
>>>>>> B
>>>>>> N
>>>>>> ATOM 331 C8 DA D 17 -5.629 -1.939 -5.291 1.00 88.65
>>>>>> B
>>>>>> C
>>>>>> ATOM 332 N7 DA D 17 -4.675 -2.838 -5.256 1.00 87.91
>>>>>> B
>>>>>> N
>>>>>> ATOM 333 C5 DA D 17 -4.574 -3.164 -3.911 1.00 87.74
>>>>>> B
>>>>>> C
>>>>>> ATOM 334 C6 DA D 17 -3.747 -4.062 -3.215 1.00 87.54
>>>>>> B
>>>>>> C
>>>>>> ATOM 335 N6 DA D 17 -2.828 -4.830 -3.804 1.00 87.21
>>>>>> B
>>>>>> N
>>>>>> ATOM 336 N1 DA D 17 -3.900 -4.147 -1.875 1.00 87.65
>>>>>> B
>>>>>> N
>>>>>> ATOM 337 C2 DA D 17 -4.826 -3.381 -1.286 1.00 87.93
>>>>>> B
>>>>>> C
>>>>>> ATOM 338 N3 DA D 17 -5.664 -2.502 -1.831 1.00 88.02
>>>>>> B
>>>>>> N
>>>>>> ATOM 339 C4 DA D 17 -5.485 -2.440 -3.162 1.00 88.27
>>>>>> B
>>>>>> C
>>>>>> ATOM 340 P DC D 18 -8.904 3.290 -3.312 1.00 95.77
>>>>>> B
>>>>>> P
>>>>>> ATOM 341 OP1 DC D 18 -10.250 3.816 -3.657 1.00 95.77
>>>>>> B
>>>>>> O
>>>>>> ATOM 342 OP2 DC D 18 -7.723 3.716 -4.106 1.00 95.96
>>>>>> B
>>>>>> O
>>>>>> ATOM 343 O5' DC D 18 -8.625 3.610 -1.778 1.00 95.50
>>>>>> B
>>>>>> O
>>>>>> ATOM 344 C5' DC D 18 -9.298 2.881 -0.755 1.00 95.41
>>>>>> B
>>>>>> C
>>>>>> ATOM 345 C4' DC D 18 -8.313 2.423 0.295 1.00 95.42
>>>>>> B
>>>>>> C
>>>>>> ATOM 346 O4' DC D 18 -7.378 1.478 -0.284 1.00 94.63
>>>>>> B
>>>>>> O
>>>>>> ATOM 347 C3' DC D 18 -7.462 3.540 0.901 1.00 95.93
>>>>>> B
>>>>>> C
>>>>>> ATOM 348 O3' DC D 18 -7.269 3.298 2.295 1.00 96.90
>>>>>> B
>>>>>> O
>>>>>> ATOM 349 C2' DC D 18 -6.136 3.399 0.178 1.00 95.31
>>>>>> B
>>>>>> C
>>>>>> ATOM 350 C1' DC D 18 -6.053 1.897 -0.001 1.00 94.14
>>>>>> B
>>>>>> C
>>>>>> ATOM 351 N1 DC D 18 -5.180 1.447 -1.097 1.00 92.96
>>>>>> B
>>>>>> N
>>>>>> ATOM 352 C2 DC D 18 -4.342 0.350 -0.877 1.00 92.64
>>>>>> B
>>>>>> C
>>>>>> ATOM 353 O2 DC D 18 -4.369 -0.213 0.227 1.00 92.96
>>>>>> B
>>>>>> O
>>>>>> ATOM 354 N3 DC D 18 -3.525 -0.068 -1.869 1.00 92.15
>>>>>> B
>>>>>> N
>>>>>> ATOM 355 C4 DC D 18 -3.524 0.564 -3.043 1.00 91.67
>>>>>> B
>>>>>> C
>>>>>> ATOM 356 N4 DC D 18 -2.699 0.118 -3.990 1.00 91.04
>>>>>> B
>>>>>> N
>>>>>> ATOM 357 C5 DC D 18 -4.371 1.683 -3.297 1.00 91.89
>>>>>> B
>>>>>> C
>>>>>> ATOM 358 C6 DC D 18 -5.177 2.087 -2.305 1.00 92.45
>>>>>> B
>>>>>> C
>>>>>> ATOM 359 P DG D 19 -6.939 4.523 3.278 1.00 97.83
>>>>>> B
>>>>>> P
>>>>>> ATOM 360 OP1 DG D 19 -8.218 4.973 3.884 1.00 98.00
>>>>>> B
>>>>>> O
>>>>>> ATOM 361 OP2 DG D 19 -6.092 5.498 2.542 1.00 98.17
>>>>>> B
>>>>>> O
>>>>>> ATOM 362 O5' DG D 19 -6.056 3.855 4.421 1.00 98.11
>>>>>> B
>>>>>> O
>>>>>> ATOM 363 C5' DG D 19 -6.504 2.685 5.102 1.00 97.58
>>>>>> B
>>>>>> C
>>>>>> ATOM 364 C4' DG D 19 -5.321 1.913 5.636 1.00 97.53
>>>>>> B
>>>>>> C
>>>>>> ATOM 365 O4' DG D 19 -4.583 1.332 4.533 1.00 96.87
>>>>>> B
>>>>>> O
>>>>>> ATOM 366 C3' DG D 19 -4.320 2.773 6.407 1.00 97.97
>>>>>> B
>>>>>> C
>>>>>> ATOM 367 O3' DG D 19 -3.783 2.045 7.513 1.00 98.86
>>>>>> B
>>>>>> O
>>>>>> ATOM 368 C2' DG D 19 -3.233 3.049 5.386 1.00 97.34
>>>>>> B
>>>>>> C
>>>>>> ATOM 369 C1' DG D 19 -3.234 1.774 4.566 1.00 96.54
>>>>>> B
>>>>>> C
>>>>>> ATOM 370 N9 DG D 19 -2.786 1.956 3.189 1.00 95.90
>>>>>> B
>>>>>> N
>>>>>> ATOM 371 C8 DG D 19 -3.212 2.910 2.294 1.00 95.66
>>>>>> B
>>>>>> C
>>>>>> ATOM 372 N7 DG D 19 -2.617 2.826 1.135 1.00 95.27
>>>>>> B
>>>>>> N
>>>>>> ATOM 373 C5 DG D 19 -1.748 1.752 1.272 1.00 94.74
>>>>>> B
>>>>>> C
>>>>>> ATOM 374 C6 DG D 19 -0.836 1.182 0.344 1.00 94.44
>>>>>> B
>>>>>> C
>>>>>> ATOM 375 O6 DG D 19 -0.604 1.526 -0.821 1.00 93.97
>>>>>> B
>>>>>> O
>>>>>> ATOM 376 N1 DG D 19 -0.153 0.103 0.898 1.00 94.09
>>>>>> B
>>>>>> N
>>>>>> ATOM 377 C2 DG D 19 -0.323 -0.367 2.177 1.00 94.43
>>>>>> B
>>>>>> C
>>>>>> ATOM 378 N2 DG D 19 0.431 -1.420 2.526 1.00 94.51
>>>>>> B
>>>>>> N
>>>>>> ATOM 379 N3 DG D 19 -1.168 0.154 3.049 1.00 94.60
>>>>>> B
>>>>>> N
>>>>>> ATOM 380 C4 DG D 19 -1.843 1.203 2.533 1.00 95.05
>>>>>> B
>>>>>> C
>>>>>> ATOM 381 P DA D 20 -2.840 2.797 8.574 1.00 99.48
>>>>>> B
>>>>>> P
>>>>>> ATOM 382 OP1 DA D 20 -3.380 2.514 9.928 1.00 99.59
>>>>>> B
>>>>>> O
>>>>>> ATOM 383 OP2 DA D 20 -2.664 4.205 8.132 1.00 99.40
>>>>>> B
>>>>>> O
>>>>>> ATOM 384 O5' DA D 20 -1.442 2.051 8.425 1.00 98.59
>>>>>> B
>>>>>> O
>>>>>> ATOM 385 C5' DA D 20 -1.342 0.644 8.631 1.00 97.42
>>>>>> B
>>>>>> C
>>>>>> ATOM 386 C4' DA D 20 0.045 0.164 8.277 1.00 96.69
>>>>>> B
>>>>>> C
>>>>>> ATOM 387 O4' DA D 20 0.248 0.270 6.845 1.00 96.10
>>>>>> B
>>>>>> O
>>>>>> ATOM 388 C3' DA D 20 1.171 0.972 8.923 1.00 96.56
>>>>>> B
>>>>>> C
>>>>>> ATOM 389 O3' DA D 20 2.238 0.101 9.310 1.00 97.28
>>>>>> B
>>>>>> O
>>>>>> ATOM 390 C2' DA D 20 1.613 1.903 7.810 1.00 95.87
>>>>>> B
>>>>>> C
>>>>>> ATOM 391 C1' DA D 20 1.417 1.033 6.585 1.00 95.04
>>>>>> B
>>>>>> C
>>>>>> ATOM 392 N9 DA D 20 1.216 1.774 5.339 1.00 93.50
>>>>>> B
>>>>>> N
>>>>>> ATOM 393 C8 DA D 20 0.310 2.774 5.079 1.00 92.81
>>>>>> B
>>>>>> C
>>>>>> ATOM 394 N7 DA D 20 0.389 3.255 3.861 1.00 92.27
>>>>>> B
>>>>>> N
>>>>>> ATOM 395 C5 DA D 20 1.413 2.520 3.278 1.00 91.68
>>>>>> B
>>>>>> C
>>>>>> ATOM 396 C6 DA D 20 1.989 2.547 1.991 1.00 90.87
>>>>>> B
>>>>>> C
>>>>>> ATOM 397 N6 DA D 20 1.601 3.378 1.021 1.00 89.73
>>>>>> B
>>>>>> N
>>>>>> ATOM 398 N1 DA D 20 2.991 1.678 1.734 1.00 90.41
>>>>>> B
>>>>>> N
>>>>>> ATOM 399 C2 DA D 20 3.383 0.846 2.706 1.00 90.63
>>>>>> B
>>>>>> C
>>>>>> ATOM 400 N3 DA D 20 2.924 0.727 3.951 1.00 91.27
>>>>>> B
>>>>>> N
>>>>>> ATOM 401 C4 DA D 20 1.929 1.602 4.176 1.00 92.11
>>>>>> B
>>>>>> C
>>>>>> ATOM 402 P DT D 21 3.710 0.701 9.552 1.00 97.60
>>>>>> B
>>>>>> P
>>>>>> ATOM 403 OP1 DT D 21 4.507 -0.337 10.254 1.00 97.36
>>>>>> B
>>>>>> O
>>>>>> ATOM 404 OP2 DT D 21 3.582 2.057 10.147 1.00 97.59
>>>>>> B
>>>>>> O
>>>>>> ATOM 405 O5' DT D 21 4.292 0.854 8.078 1.00 96.51
>>>>>> B
>>>>>> O
>>>>>> ATOM 406 C5' DT D 21 4.650 -0.296 7.314 1.00 95.17
>>>>>> B
>>>>>> C
>>>>>> ATOM 407 C4' DT D 21 5.842 0.016 6.442 1.00 94.15
>>>>>> B
>>>>>> C
>>>>>> ATOM 408 O4' DT D 21 5.430 0.811 5.303 1.00 93.46
>>>>>> B
>>>>>> O
>>>>>> ATOM 409 C3' DT D 21 6.915 0.828 7.165 1.00 93.74
>>>>>> B
>>>>>> C
>>>>>> ATOM 410 O3' DT D 21 8.220 0.390 6.788 1.00 93.61
>>>>>> B
>>>>>> O
>>>>>> ATOM 411 C2' DT D 21 6.669 2.246 6.684 1.00 93.39
>>>>>> B
>>>>>> C
>>>>>> ATOM 412 C1' DT D 21 6.166 2.025 5.267 1.00 92.51
>>>>>> B
>>>>>> C
>>>>>> ATOM 413 N1 DT D 21 5.272 3.083 4.754 1.00 90.87
>>>>>> B
>>>>>> N
>>>>>> ATOM 414 C2 DT D 21 5.404 3.458 3.436 1.00 90.11
>>>>>> B
>>>>>> C
>>>>>> ATOM 415 O2 DT D 21 6.222 2.959 2.680 1.00 89.73
>>>>>> B
>>>>>> O
>>>>>> ATOM 416 N3 DT D 21 4.537 4.444 3.032 1.00 89.28
>>>>>> B
>>>>>> N
>>>>>> ATOM 417 C4 DT D 21 3.575 5.076 3.797 1.00 89.12
>>>>>> B
>>>>>> C
>>>>>> ATOM 418 O4 DT D 21 2.864 5.942 3.293 1.00 88.52
>>>>>> B
>>>>>> O
>>>>>> ATOM 419 C5 DT D 21 3.495 4.637 5.170 1.00 89.42
>>>>>> B
>>>>>> C
>>>>>> ATOM 420 C7 DT D 21 2.485 5.268 6.075 1.00 89.83
>>>>>> B
>>>>>> C
>>>>>> ATOM 421 C6 DT D 21 4.335 3.675 5.575 1.00 90.06
>>>>>> B
>>>>>> C
>>>>>> ATOM 422 P DG D 22 9.392 0.366 7.885 1.00 93.81
>>>>>> B
>>>>>> P
>>>>>> ATOM 423 OP1 DG D 22 9.638 -1.055 8.246 1.00 93.20
>>>>>> B
>>>>>> O
>>>>>> ATOM 424 OP2 DG D 22 9.053 1.348 8.948 1.00 93.20
>>>>>> B
>>>>>> O
>>>>>> ATOM 425 O5' DG D 22 10.661 0.907 7.093 1.00 91.48
>>>>>> B
>>>>>> O
>>>>>> ATOM 426 C5' DG D 22 11.196 0.189 5.985 1.00 87.91
>>>>>> B
>>>>>> C
>>>>>> ATOM 427 C4' DG D 22 11.955 1.131 5.081 1.00 85.46
>>>>>> B
>>>>>> C
>>>>>> ATOM 428 O4' DG D 22 11.020 1.965 4.349 1.00 84.64
>>>>>> B
>>>>>> O
>>>>>> ATOM 429 C3' DG D 22 12.881 2.087 5.832 1.00 84.00
>>>>>> B
>>>>>> C
>>>>>> ATOM 430 O3' DG D 22 14.107 2.256 5.119 1.00 82.18
>>>>>> B
>>>>>> O
>>>>>> ATOM 431 C2' DG D 22 12.094 3.384 5.872 1.00 83.72
>>>>>> B
>>>>>> C
>>>>>> ATOM 432 C1' DG D 22 11.316 3.336 4.570 1.00 83.63
>>>>>> B
>>>>>> C
>>>>>> ATOM 433 N9 DG D 22 10.054 4.070 4.618 1.00 82.70
>>>>>> B
>>>>>> N
>>>>>> ATOM 434 C8 DG D 22 9.223 4.206 5.704 1.00 82.33
>>>>>> B
>>>>>> C
>>>>>> ATOM 435 N7 DG D 22 8.172 4.940 5.458 1.00 82.14
>>>>>> B
>>>>>> N
>>>>>> ATOM 436 C5 DG D 22 8.313 5.309 4.127 1.00 81.36
>>>>>> B
>>>>>> C
>>>>>> ATOM 437 C6 DG D 22 7.479 6.112 3.303 1.00 80.72
>>>>>> B
>>>>>> C
>>>>>> ATOM 438 O6 DG D 22 6.417 6.677 3.596 1.00 79.24
>>>>>> B
>>>>>> O
>>>>>> ATOM 439 N1 DG D 22 7.996 6.231 2.017 1.00 80.26
>>>>>> B
>>>>>> N
>>>>>> ATOM 440 C2 DG D 22 9.163 5.656 1.577 1.00 80.55
>>>>>> B
>>>>>> C
>>>>>> ATOM 441 N2 DG D 22 9.489 5.891 0.298 1.00 80.16
>>>>>> B
>>>>>> N
>>>>>> ATOM 442 N3 DG D 22 9.951 4.907 2.336 1.00 81.28
>>>>>> B
>>>>>> N
>>>>>> ATOM 443 C4 DG D 22 9.468 4.777 3.591 1.00 81.91
>>>>>> B
>>>>>> C
>>>>>> ATOM 444 P DG D 23 15.023 3.545 5.404 1.00 80.62
>>>>>> B
>>>>>> P
>>>>>> ATOM 445 OP1 DG D 23 16.425 3.168 5.089 1.00 80.76
>>>>>> B
>>>>>> O
>>>>>> ATOM 446 OP2 DG D 23 14.693 4.092 6.746 1.00 80.49
>>>>>> B
>>>>>> O
>>>>>> ATOM 447 O5' DG D 23 14.535 4.582 4.300 1.00 77.74
>>>>>> B
>>>>>> O
>>>>>> ATOM 448 C5' DG D 23 14.617 4.251 2.916 1.00 72.46
>>>>>> B
>>>>>> C
>>>>>> ATOM 449 C4' DG D 23 14.582 5.505 2.078 1.00 68.88
>>>>>> B
>>>>>> C
>>>>>> ATOM 450 O4' DG D 23 13.235 6.038 2.030 1.00 67.18
>>>>>> B
>>>>>> O
>>>>>> ATOM 451 C3' DG D 23 15.467 6.631 2.615 1.00 67.17
>>>>>> B
>>>>>> C
>>>>>> ATOM 452 O3' DG D 23 16.088 7.318 1.530 1.00 66.13
>>>>>> B
>>>>>> O
>>>>>> ATOM 453 C2' DG D 23 14.476 7.548 3.307 1.00 66.53
>>>>>> B
>>>>>> C
>>>>>> ATOM 454 C1' DG D 23 13.259 7.401 2.417 1.00 65.49
>>>>>> B
>>>>>> C
>>>>>> ATOM 455 N9 DG D 23 11.992 7.720 3.066 1.00 63.24
>>>>>> B
>>>>>> N
>>>>>> ATOM 456 C8 DG D 23 11.589 7.368 4.333 1.00 62.14
>>>>>> B
>>>>>> C
>>>>>> ATOM 457 N7 DG D 23 10.415 7.843 4.647 1.00 61.17
>>>>>> B
>>>>>> N
>>>>>> ATOM 458 C5 DG D 23 10.013 8.543 3.516 1.00 61.08
>>>>>> B
>>>>>> C
>>>>>> ATOM 459 C6 DG D 23 8.827 9.283 3.262 1.00 60.15
>>>>>> B
>>>>>> C
>>>>>> ATOM 460 O6 DG D 23 7.864 9.480 4.014 1.00 59.71
>>>>>> B
>>>>>> O
>>>>>> ATOM 461 N1 DG D 23 8.828 9.828 1.981 1.00 59.42
>>>>>> B
>>>>>> N
>>>>>> ATOM 462 C2 DG D 23 9.839 9.686 1.062 1.00 59.73
>>>>>> B
>>>>>> C
>>>>>> ATOM 463 N2 DG D 23 9.655 10.292 -0.121 1.00 58.12
>>>>>> B
>>>>>> N
>>>>>> ATOM 464 N3 DG D 23 10.950 9.001 1.287 1.00 60.71
>>>>>> B
>>>>>> N
>>>>>> ATOM 465 C4 DG D 23 10.970 8.463 2.526 1.00 61.97
>>>>>> B
>>>>>> C
>>>>>> ATOM 466 P DG D 24 17.085 8.541 1.828 1.00 65.57
>>>>>> B
>>>>>> P
>>>>>> ATOM 467 OP1 DG D 24 18.403 8.167 1.256 1.00 65.25
>>>>>> B
>>>>>> O
>>>>>> ATOM 468 OP2 DG D 24 16.985 8.910 3.265 1.00 64.97
>>>>>> B
>>>>>> O
>>>>>> ATOM 469 O5' DG D 24 16.476 9.728 0.956 1.00 61.93
>>>>>> B
>>>>>> O
>>>>>> ATOM 470 C5' DG D 24 16.262 9.557 -0.445 1.00 56.81
>>>>>> B
>>>>>> C
>>>>>> ATOM 471 C4' DG D 24 15.661 10.807 -1.046 1.00 52.96
>>>>>> B
>>>>>> C
>>>>>> ATOM 472 O4' DG D 24 14.286 10.956 -0.616 1.00 51.17
>>>>>> B
>>>>>> O
>>>>>> ATOM 473 C3' DG D 24 16.368 12.106 -0.663 1.00 52.01
>>>>>> B
>>>>>> C
>>>>>> ATOM 474 O3' DG D 24 16.262 13.036 -1.741 1.00 49.61
>>>>>> B
>>>>>> O
>>>>>> ATOM 475 C2' DG D 24 15.516 12.628 0.479 1.00 50.65
>>>>>> B
>>>>>> C
>>>>>> ATOM 476 C1' DG D 24 14.121 12.196 0.052 1.00 50.16
>>>>>> B
>>>>>> C
>>>>>> ATOM 477 N9 DG D 24 13.187 11.991 1.156 1.00 48.36
>>>>>> B
>>>>>> N
>>>>>> ATOM 478 C8 DG D 24 13.352 11.157 2.238 1.00 47.26
>>>>>> B
>>>>>> C
>>>>>> ATOM 479 N7 DG D 24 12.356 11.209 3.081 1.00 45.80
>>>>>> B
>>>>>> N
>>>>>> ATOM 480 C5 DG D 24 11.476 12.128 2.521 1.00 46.49
>>>>>> B
>>>>>> C
>>>>>> ATOM 481 C6 DG D 24 10.221 12.610 2.989 1.00 46.23
>>>>>> B
>>>>>> C
>>>>>> ATOM 482 O6 DG D 24 9.621 12.320 4.032 1.00 45.56
>>>>>> B
>>>>>> O
>>>>>> ATOM 483 N1 DG D 24 9.666 13.530 2.105 1.00 45.52
>>>>>> B
>>>>>> N
>>>>>> ATOM 484 C2 DG D 24 10.239 13.941 0.928 1.00 44.77
>>>>>> B
>>>>>> C
>>>>>> ATOM 485 N2 DG D 24 9.539 14.833 0.214 1.00 45.10
>>>>>> B
>>>>>> N
>>>>>> ATOM 486 N3 DG D 24 11.409 13.510 0.485 1.00 46.25
>>>>>> B
>>>>>> N
>>>>>> ATOM 487 C4 DG D 24 11.969 12.611 1.326 1.00 47.23
>>>>>> B
>>>>>> C
>>>>>> TER
>>>>>>
>>>>>> Note that each chain is defined as a separate chain and there is a TER
>>>>>> between the both. Next I use the following script for parameterization
>>>>>> using tleap:
>>>>>>
>>>>>> #source leaprc.protein.ff19SB < uncoment for a protein in the system
>>>>>> source leaprc.water.opc
>>>>>> #source leaprc.gaff < uncoment for a small compound in the system
>>>>>> source leaprc.DNA.bsc1
>>>>>> prot = loadpdb ./proc.pdb
>>>>>> addIons prot Cl- 0
>>>>>> addIons prot Na+ 0
>>>>>> setbox prot centers
>>>>>> solvateoct prot TIP3PBOX 15.0
>>>>>> savepdb prot ./test.pdb
>>>>>> saveamberparm prot ./test.prmtop ./test.prmcrd
>>>>>> quit
>>>>>>
>>>>>> according to log it adds some additional atoms to DNA (probably in the
>>>>>> interphase between chains C and D:
>>>>>>
>>>>>> Parmbsc1 force-field for DNA
>>>>>> Loading PDB file: ./proc.pdb
>>>>>> (starting new molecule for chain D)
>>>>>> Created a new atom named: P within residue: .R<DC5 1>
>>>>>> Created a new atom named: OP1 within residue: .R<DC5 1>
>>>>>> Created a new atom named: OP2 within residue: .R<DC5 1>
>>>>>> total atoms in file: 6175
>>>>>>
>>>>>> but then it indicates that these atoms are wrong:
>>>>>>
>>>>>> Checking Unit.
>>>>>> FATAL: Atom .R<DC5 1>.A<P 29> does not have a type.
>>>>>> FATAL: Atom .R<DC5 1>.A<OP1 30> does not have a type.
>>>>>> FATAL: Atom .R<DC5 1>.A<OP2 31> does not have a type.
>>>>>>
>>>>>> /opt/site/ubuntu_22.04/amber/22b/bin/teLeap: Fatal Error!
>>>>>>
>>>>>> How could it be fixed?
>>>>>>
>>>>>> Yours with thanks
>>>>>>
>>>>>> Enrico
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
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Received on Mon Apr 22 2024 - 09:00:02 PDT
