Re: pair.pdb and cutoff for pairInteraction

From: Shirley Li (li19104_at_yahoo.com)
Date: Tue Nov 29 2005 - 22:33:36 CST

  Dear Peter,
   
  Thank you so much for your detailed explaination and the sample file. Those really help a lot. I have some further questioins:
   
  1) I wonder how the force is defined and correlated to energy. Does positive force means repulsive and negative means attractive interaction?
  2) I was computing the interaction of two groups of atoms. I got positive VDW force most of the time, while the VDW energy is negative all the time. Should VDW energy always have the same sign with VDW force, both positive or both negative? How about Electrostatics?
   
  Thank you again for youur kind help.
   
  Best regards,
   
  Shirley

Peter Freddolino <petefred_at_ks.uiuc.edu> wrote: Dear Shirley,

>
> 1) For the pair.pdb file, I'm not clear about the "B column". Could
> sb give me a sample pair.pdb file?

The B-column refers to the beta field of a pdb file, columns 62-66. In
the attached pdb file, the beta field for protein atoms is 1, and for
water atoms is 2.

> 2) Is there any way to set a distance cutoff, so that any atom in one
> group falls beyond the cutoff from the other group will be ignored for
> consideration of the calculation?

This will be based on your nonbond cutoff, so you should set that cutoff
accordingly.

> 3) To execute the calculation, should I prepare a conf file as usual,
> and submit the NAMD job?
>
This is correct; you should just use "run 0" instead of the usual run
command.

Please let me know if this is not clear.
Peter

CRYST1 50.840 42.770 28.950 90.00 90.00 90.00 P 1 1
ATOM 1 N MET X 1 27.340 24.430 2.614 0.00 1.00 1UBQ
ATOM 2 CA MET X 1 26.266 25.413 2.842 0.00 1.00 1UBQ
ATOM 3 C MET X 1 26.913 26.639 3.531 0.00 1.00 1UBQ
ATOM 4 O MET X 1 27.886 26.463 4.263 0.00 1.00 1UBQ
ATOM 5 CB MET X 1 25.112 24.880 3.649 0.00 1.00 1UBQ
ATOM 6 CG MET X 1 25.353 24.860 5.134 0.00 1.00 1UBQ
ATOM 7 SD MET X 1 23.930 23.959 5.904 0.00 1.00 1UBQ
ATOM 8 CE MET X 1 24.447 23.984 7.620 0.00 1.00 1UBQ
ATOM 9 N GLN X 2 26.335 27.770 3.258 0.00 1.00 1UBQ
ATOM 10 CA GLN X 2 26.850 29.021 3.898 0.00 1.00 1UBQ
ATOM 11 C GLN X 2 26.100 29.253 5.202 0.00 1.00 1UBQ
ATOM 12 O GLN X 2 24.865 29.024 5.330 0.00 1.00 1UBQ
ATOM 13 CB GLN X 2 26.733 30.148 2.905 0.00 1.00 1UBQ
ATOM 14 CG GLN X 2 26.882 31.546 3.409 0.00 1.00 1UBQ
ATOM 15 CD GLN X 2 26.786 32.562 2.270 0.00 1.00 1UBQ
ATOM 16 OE1 GLN X 2 27.783 33.160 1.870 0.00 1.00 1UBQ
ATOM 17 NE2 GLN X 2 25.562 32.733 1.806 0.00 1.00 1UBQ
ATOM 18 N ILE X 3 26.849 29.656 6.217 0.00 1.00 1UBQ
ATOM 19 CA ILE X 3 26.235 30.058 7.497 0.00 1.00 1UBQ
ATOM 20 C ILE X 3 26.882 31.428 7.862 0.00 1.00 1UBQ
ATOM 21 O ILE X 3 27.906 31.711 7.264 0.00 1.00 1UBQ
ATOM 22 CB ILE X 3 26.344 29.050 8.645 0.00 1.00 1UBQ
ATOM 23 CG1 ILE X 3 27.810 28.748 8.999 0.00 1.00 1UBQ
ATOM 24 CG2 ILE X 3 25.491 27.771 8.287 0.00 1.00 1UBQ
ATOM 25 CD1 ILE X 3 27.967 28.087 10.417 0.00 1.00 1UBQ
ATOM 26 N PHE X 4 26.214 32.097 8.771 0.00 1.00 1UBQ
ATOM 27 CA PHE X 4 26.772 33.436 9.197 0.00 1.00 1UBQ
ATOM 28 C PHE X 4 27.151 33.362 10.650 0.00 1.00 1UBQ
ATOM 29 O PHE X 4 26.350 32.778 11.395 0.00 1.00 1UBQ
ATOM 30 CB PHE X 4 25.695 34.498 8.946 0.00 1.00 1UBQ
ATOM 31 CG PHE X 4 25.288 34.609 7.499 0.00 1.00 1UBQ
ATOM 32 CD1 PHE X 4 24.147 33.966 7.038 0.00 1.00 1UBQ
ATOM 33 CD2 PHE X 4 26.136 35.346 6.640 0.00 1.00 1UBQ
ATOM 34 CE1 PHE X 4 23.812 34.031 5.677 0.00 1.00 1UBQ
ATOM 35 CE2 PHE X 4 25.810 35.392 5.267 0.00 1.00 1UBQ
ATOM 36 CZ PHE X 4 24.620 34.778 4.853 0.00 1.00 1UBQ
ATOM 37 N VAL X 5 28.260 33.943 11.096 0.00 1.00 1UBQ
ATOM 38 CA VAL X 5 28.605 33.965 12.503 0.00 1.00 1UBQ
ATOM 39 C VAL X 5 28.638 35.461 12.900 0.00 1.00 1UBQ
ATOM 40 O VAL X 5 29.522 36.103 12.320 0.00 1.00 1UBQ
ATOM 41 CB VAL X 5 29.963 33.317 12.814 0.00 1.00 1UBQ
ATOM 42 CG1 VAL X 5 30.211 33.394 14.304 0.00 1.00 1UBQ
ATOM 43 CG2 VAL X 5 29.957 31.838 12.352 0.00 1.00 1UBQ
ATOM 44 N LYS X 6 27.751 35.867 13.740 0.00 1.00 1UBQ
ATOM 45 CA LYS X 6 27.691 37.315 14.143 0.00 1.00 1UBQ
ATOM 46 C LYS X 6 28.469 37.475 15.420 0.00 1.00 1UBQ
ATOM 47 O LYS X 6 28.213 36.753 16.411 0.00 1.00 1UBQ
ATOM 48 CB LYS X 6 26.219 37.684 14.307 0.00 1.00 1UBQ
ATOM 49 CG LYS X 6 25.884 39.139 14.615 0.00 1.00 1UBQ
ATOM 50 CD LYS X 6 24.348 39.296 14.642 0.00 1.00 1UBQ
ATOM 51 CE LYS X 6 23.865 40.723 14.749 0.00 1.00 1UBQ
ATOM 52 NZ LYS X 6 22.375 40.720 14.907 0.00 1.00 1UBQ
ATOM 53 N THR X 7 29.426 38.430 15.446 0.00 1.00 1UBQ
ATOM 54 CA THR X 7 30.225 38.643 16.662 0.00 1.00 1UBQ
ATOM 55 C THR X 7 29.664 39.839 17.434 0.00 1.00 1UBQ
ATOM 56 O THR X 7 28.850 40.565 16.859 0.00 1.00 1UBQ
ATOM 57 CB THR X 7 31.744 38.879 16.299 0.00 1.00 1UBQ
ATOM 58 OG1 THR X 7 31.737 40.257 15.824 0.00 1.00 1UBQ
ATOM 59 CG2 THR X 7 32.260 37.969 15.171 0.00 1.00 1UBQ
ATOM 60 N LEU X 8 30.132 40.069 18.642 0.00 1.00 1UBQ
ATOM 61 CA LEU X 8 29.607 41.180 19.467 0.00 1.00 1UBQ
ATOM 62 C LEU X 8 30.075 42.538 18.984 0.00 1.00 1UBQ
ATOM 63 O LEU X 8 29.586 43.570 19.483 0.00 1.00 1UBQ
ATOM 64 CB LEU X 8 29.919 40.890 20.938 0.00 1.00 1UBQ
ATOM 65 CG LEU X 8 29.183 39.722 21.581 0.00 1.00 1UBQ
ATOM 66 CD1 LEU X 8 29.308 39.750 23.095 0.00 1.00 1UBQ
ATOM 67 CD2 LEU X 8 27.700 39.721 21.228 0.00 1.00 1UBQ
ATOM 68 N THR X 9 30.991 42.571 17.998 0.00 1.00 1UBQ
ATOM 69 CA THR X 9 31.422 43.940 17.553 0.00 1.00 1UBQ
ATOM 70 C THR X 9 30.755 44.351 16.277 0.00 1.00 1UBQ
ATOM 71 O THR X 9 31.207 45.268 15.566 0.00 1.00 1UBQ
ATOM 72 CB THR X 9 32.979 43.918 17.445 0.00 1.00 1UBQ
ATOM 73 OG1 THR X 9 33.174 43.067 16.265 0.00 1.00 1UBQ
ATOM 74 CG2 THR X 9 33.657 43.319 18.672 0.00 1.00 1UBQ
ATOM 75 N GLY X 10 29.721 43.673 15.885 0.00 1.00 1UBQ
ATOM 76 CA GLY X 10 28.978 43.960 14.678 0.00 1.00 1UBQ
ATOM 77 C GLY X 10 29.604 43.507 13.393 0.00 1.00 1UBQ
ATOM 78 O GLY X 10 29.219 43.981 12.301 0.00 1.00 1UBQ
ATOM 79 N LYS X 11 30.563 42.623 13.495 0.00 1.00 1UBQ
ATOM 80 CA LYS X 11 31.191 42.012 12.331 0.00 1.00 1UBQ
ATOM 81 C LYS X 11 30.459 40.666 12.130 0.00 1.00 1UBQ
ATOM 82 O LYS X 11 30.253 39.991 13.133 0.00 1.00 1UBQ
ATOM 83 CB LYS X 11 32.672 41.717 12.505 0.00 1.00 1UBQ
ATOM 84 CG LYS X 11 33.280 41.086 11.227 0.00 1.00 1UBQ
ATOM 85 CD LYS X 11 34.762 40.799 11.470 0.00 1.00 1UBQ
ATOM 86 CE LYS X 11 35.614 40.847 10.240 0.00 1.00 1UBQ
ATOM 87 NZ LYS X 11 35.100 40.073 9.101 0.00 1.00 1UBQ
ATOM 88 N THR X 12 30.163 40.338 10.886 0.00 1.00 1UBQ
ATOM 89 CA THR X 12 29.542 39.020 10.653 0.00 1.00 1UBQ
ATOM 90 C THR X 12 30.494 38.261 9.729 0.00 1.00 1UBQ
ATOM 91 O THR X 12 30.849 38.850 8.706 0.00 1.00 1UBQ
ATOM 92 CB THR X 12 28.113 39.049 10.015 0.00 1.00 1UBQ
ATOM 93 OG1 THR X 12 27.280 39.722 10.996 0.00 1.00 1UBQ
ATOM 94 CG2 THR X 12 27.588 37.635 9.715 0.00 1.00 1UBQ
ATOM 95 N ILE X 13 30.795 37.015 10.095 0.00 1.00 1UBQ
ATOM 96 CA ILE X 13 31.720 36.289 9.176 0.00 1.00 1UBQ
ATOM 97 C ILE X 13 30.955 35.211 8.459 0.00 1.00 1UBQ
ATOM 98 O ILE X 13 30.025 34.618 9.040 0.00 1.00 1UBQ
ATOM 99 CB ILE X 13 32.995 35.883 9.934 0.00 1.00 1UBQ
ATOM 100 CG1 ILE X 13 33.306 34.381 9.840 0.00 1.00 1UBQ
ATOM 101 CG2 ILE X 13 33.109 36.381 11.435 0.00 1.00 1UBQ
ATOM 102 CD1 ILE X 13 34.535 34.028 10.720 0.00 1.00 1UBQ
ATOM 103 N THR X 14 31.244 34.986 7.197 0.00 1.00 1UBQ
ATOM 104 CA THR X 14 30.505 33.884 6.512 0.00 1.00 1UBQ
ATOM 105 C THR X 14 31.409 32.680 6.446 0.00 1.00 1UBQ
ATOM 106 O THR X 14 32.619 32.812 6.125 0.00 1.00 1UBQ
ATOM 107 CB THR X 14 30.091 34.393 5.078 0.00 1.00 1UBQ
ATOM 108 OG1 THR X 14 31.440 34.513 4.487 0.00 1.00 1UBQ
ATOM 109 CG2 THR X 14 29.420 35.756 5.119 0.00 1.00 1UBQ
ATOM 110 N LEU X 15 30.884 31.485 6.666 0.00 1.00 1UBQ
ATOM 111 CA LEU X 15 31.677 30.275 6.639 0.00 1.00 1UBQ
ATOM 112 C LEU X 15 31.022 29.288 5.665 0.00 1.00 1UBQ
ATOM 113 O LEU X 15 29.809 29.395 5.545 0.00 1.00 1UBQ
ATOM 114 CB LEU X 15 31.562 29.686 8.045 0.00 1.00 1UBQ
ATOM 115 CG LEU X 15 32.631 29.444 9.060 0.00 1.00 1UBQ
ATOM 116 CD1 LEU X 15 33.814 30.390 9.030 0.00 1.00 1UBQ
ATOM 117 CD2 LEU X 15 31.945 29.449 10.436 0.00 1.00 1UBQ
ATOM 118 N GLU X 16 31.834 28.412 5.125 0.00 1.00 1UBQ
ATOM 119 CA GLU X 16 31.220 27.341 4.275 0.00 1.00 1UBQ
ATOM 120 C GLU X 16 31.440 26.079 5.080 0.00 1.00 1UBQ
ATOM 121 O GLU X 16 32.576 25.802 5.461 0.00 1.00 1UBQ
ATOM 122 CB GLU X 16 31.827 27.262 2.894 0.00 1.00 1UBQ
ATOM 123 CG GLU X 16 31.363 28.410 1.962 0.00 1.00 1UBQ
ATOM 124 CD GLU X 16 31.671 28.291 0.498 0.00 1.00 1UBQ
ATOM 125 OE1 GLU X 16 30.869 28.621 -0.366 0.00 1.00 1UBQ
ATOM 126 OE2 GLU X 16 32.835 27.861 0.278 0.00 1.00 1UBQ
ATOM 127 N VAL X 17 30.310 25.458 5.384 0.00 1.00 1UBQ
ATOM 128 CA VAL X 17 30.288 24.245 6.193 0.00 1.00 1UBQ
ATOM 129 C VAL X 17 29.279 23.227 5.641 0.00 1.00 1UBQ
ATOM 130 O VAL X 17 28.478 23.522 4.725 0.00 1.00 1UBQ
ATOM 131 CB VAL X 17 29.903 24.590 7.665 0.00 1.00 1UBQ
ATOM 132 CG1 VAL X 17 30.862 25.496 8.389 0.00 1.00 1UBQ
ATOM 133 CG2 VAL X 17 28.476 25.135 7.705 0.00 1.00 1UBQ
ATOM 134 N GLU X 18 29.380 22.057 6.232 0.00 1.00 1UBQ
ATOM 135 CA GLU X 18 28.468 20.940 5.980 0.00 1.00 1UBQ
ATOM 136 C GLU X 18 27.819 20.609 7.316 0.00 1.00 1UBQ
ATOM 137 O GLU X 18 28.449 20.674 8.360 0.00 1.00 1UBQ
ATOM 138 CB GLU X 18 29.213 19.697 5.506 0.00 1.00 1UBQ
ATOM 139 CG GLU X 18 29.728 19.755 4.060 0.00 1.00 1UBQ
ATOM 140 CD GLU X 18 28.754 20.061 2.978 0.00 1.00 1UBQ
ATOM 141 OE1 GLU X 18 27.546 19.992 2.985 0.00 1.00 1UBQ
ATOM 142 OE2 GLU X 18 29.336 20.423 1.904 0.00 1.00 1UBQ
ATOM 143 N PRO X 19 26.559 20.220 7.288 0.00 1.00 1UBQ
ATOM 144 CA PRO X 19 25.829 19.825 8.494 0.00 1.00 1UBQ
ATOM 145 C PRO X 19 26.541 18.732 9.251 0.00 1.00 1UBQ
ATOM 146 O PRO X 19 26.333 18.536 10.457 0.00 1.00 1UBQ
ATOM 147 CB PRO X 19 24.469 19.332 7.952 0.00 1.00 1UBQ
ATOM 148 CG PRO X 19 24.299 20.134 6.704 0.00 1.00 1UBQ
ATOM 149 CD PRO X 19 25.714 20.108 6.073 0.00 1.00 1UBQ
ATOM 150 N SER X 20 27.361 17.959 8.559 0.00 1.00 1UBQ
ATOM 151 CA SER X 20 28.054 16.835 9.210 0.00 1.00 1UBQ
ATOM 152 C SER X 20 29.258 17.318 9.984 0.00 1.00 1UBQ
ATOM 153 O SER X 20 29.930 16.477 10.606 0.00 1.00 1UBQ
ATOM 154 CB SER X 20 28.523 15.820 8.182 0.00 1.00 1UBQ
ATOM 155 OG SER X 20 28.946 16.445 6.967 0.00 1.00 1UBQ
ATOM 156 N ASP X 21 29.599 18.599 9.828 0.00 1.00 1UBQ
ATOM 157 CA ASP X 21 30.796 19.083 10.566 0.00 1.00 1UBQ
ATOM 158 C ASP X 21 30.491 19.162 12.040 0.00 1.00 1UBQ
ATOM 159 O ASP X 21 29.367 19.523 12.441 0.00 1.00 1UBQ
ATOM 160 CB ASP X 21 31.155 20.515 10.048 0.00 1.00 1UBQ
ATOM 161 CG ASP X 21 31.923 20.436 8.755 0.00 1.00 1UBQ
ATOM 162 OD1 ASP X 21 32.493 19.374 8.456 0.00 1.00 1UBQ
ATOM 163 OD2 ASP X 21 31.838 21.402 7.968 0.00 1.00 1UBQ
ATOM 164 N THR X 22 31.510 18.936 12.852 0.00 1.00 1UBQ
ATOM 165 CA THR X 22 31.398 19.064 14.286 0.00 1.00 1UBQ
ATOM 166 C THR X 22 31.593 20.553 14.655 0.00 1.00 1UBQ
ATOM 167 O THR X 22 32.159 21.311 13.861 0.00 1.00 1UBQ
ATOM 168 CB THR X 22 32.492 18.193 14.995 0.00 1.00 1UBQ
ATOM 169 OG1 THR X 22 33.778 18.739 14.516 0.00 1.00 1UBQ
ATOM 170 CG2 THR X 22 32.352 16.700 14.630 0.00 1.00 1UBQ
ATOM 171 N ILE X 23 31.113 20.863 15.860 0.00 1.00 1UBQ
ATOM 172 CA ILE X 23 31.288 22.201 16.417 0.00 1.00 1UBQ
ATOM 173 C ILE X 23 32.776 22.519 16.577 0.00 1.00 1UBQ
ATOM 174 O ILE X 23 33.233 23.659 16.384 0.00 1.00 1UBQ
ATOM 175 CB ILE X 23 30.520 22.300 17.764 0.00 1.00 1UBQ
ATOM 176 CG1 ILE X 23 29.006 22.043 17.442 0.00 1.00 1UBQ
ATOM 177 CG2 ILE X 23 30.832 23.699 18.358 0.00 1.00 1UBQ
ATOM 178 CD1 ILE X 23 28.407 22.948 16.366 0.00 1.00 1UBQ
ATOM 179 N GLU X 24 33.548 21.526 16.950 0.00 1.00 1UBQ
ATOM 180 CA GLU X 24 35.031 21.722 17.069 0.00 1.00 1UBQ
ATOM 181 C GLU X 24 35.615 22.190 15.759 0.00 1.00 1UBQ
ATOM 182 O GLU X 24 36.532 23.046 15.724 0.00 1.00 1UBQ
ATOM 183 CB GLU X 24 35.667 20.383 17.447 0.00 1.00 1UBQ
ATOM 184 CG GLU X 24 37.128 20.293 17.872 0.00 1.00 1UBQ
ATOM 185 CD GLU X 24 37.561 18.851 18.082 0.00 1.00 1UBQ
ATOM 186 OE1 GLU X 24 37.758 18.024 17.195 0.00 1.00 1UBQ
ATOM 187 OE2 GLU X 24 37.628 18.599 19.313 0.00 1.00 1UBQ
ATOM 188 N ASN X 25 35.139 21.624 14.662 0.00 1.00 1UBQ
ATOM 189 CA ASN X 25 35.590 21.945 13.302 0.00 1.00 1UBQ
ATOM 190 C ASN X 25 35.238 23.382 12.920 0.00 1.00 1UBQ
ATOM 191 O ASN X 25 36.066 24.109 12.333 0.00 1.00 1UBQ
ATOM 192 CB ASN X 25 35.064 20.957 12.255 0.00 1.00 1UBQ
ATOM 193 CG ASN X 25 35.541 21.418 10.871 0.00 1.00 1UBQ
ATOM 194 OD1 ASN X 25 36.772 21.623 10.676 0.00 1.00 1UBQ
ATOM 195 ND2 ASN X 25 34.628 21.595 9.920 0.00 1.00 1UBQ
ATOM 196 N VAL X 26 34.007 23.745 13.250 0.00 1.00 1UBQ
ATOM 197 CA VAL X 26 33.533 25.097 12.978 0.00 1.00 1UBQ
ATOM 198 C VAL X 26 34.441 26.099 13.684 0.00 1.00 1UBQ
ATOM 199 O VAL X 26 34.883 27.090 13.093 0.00 1.00 1UBQ
ATOM 200 CB VAL X 26 32.060 25.257 13.364 0.00 1.00 1UBQ
ATOM 201 CG1 VAL X 26 31.684 26.749 13.342 0.00 1.00 1UBQ
ATOM 202 CG2 VAL X 26 31.152 24.421 12.477 0.00 1.00 1UBQ
ATOM 203 N LYS X 27 34.734 25.822 14.949 0.00 1.00 1UBQ
ATOM 204 CA LYS X 27 35.596 26.715 15.736 0.00 1.00 1UBQ
ATOM 205 C LYS X 27 36.975 26.826 15.107 0.00 1.00 1UBQ
ATOM 206 O LYS X 27 37.579 27.926 15.159 0.00 1.00 1UBQ
ATOM 207 CB LYS X 27 35.715 26.203 17.172 0.00 1.00 1UBQ
ATOM 208 CG LYS X 27 34.343 26.445 17.898 0.00 1.00 1UBQ
ATOM 209 CD LYS X 27 34.509 26.077 19.360 0.00 1.00 1UBQ
ATOM 210 CE LYS X 27 33.206 26.311 20.122 0.00 1.00 1UBQ
ATOM 211 NZ LYS X 27 33.455 25.910 21.546 0.00 1.00 1UBQ
ATOM 212 N ALA X 28 37.499 25.743 14.571 0.00 1.00 1UBQ
ATOM 213 CA ALA X 28 38.794 25.761 13.880 0.00 1.00 1UBQ
ATOM 214 C ALA X 28 38.728 26.591 12.611 0.00 1.00 1UBQ
ATOM 215 O ALA X 28 39.704 27.346 12.277 0.00 1.00 1UBQ
ATOM 216 CB ALA X 28 39.285 24.336 13.566 0.00 1.00 1UBQ
ATOM 217 N LYS X 29 37.633 26.543 11.867 0.00 1.00 1UBQ
ATOM 218 CA LYS X 29 37.471 27.391 10.668 0.00 1.00 1UBQ
ATOM 219 C LYS X 29 37.441 28.882 11.052 0.00 1.00 1UBQ
ATOM 220 O LYS X 29 38.020 29.772 10.382 0.00 1.00 1UBQ
ATOM 221 CB LYS X 29 36.193 27.058 9.911 0.00 1.00 1UBQ
ATOM 222 CG LYS X 29 36.153 25.620 9.409 0.00 1.00 1UBQ
ATOM 223 CD LYS X 29 34.758 25.280 8.900 0.00 1.00 1UBQ
ATOM 224 CE LYS X 29 34.793 24.264 7.767 0.00 1.00 1UBQ
ATOM 225 NZ LYS X 29 34.914 24.944 6.441 0.00 1.00 1UBQ
ATOM 226 N ILE X 30 36.811 29.170 12.192 0.00 1.00 1UBQ
ATOM 227 CA ILE X 30 36.731 30.570 12.645 0.00 1.00 1UBQ
ATOM 228 C ILE X 30 38.148 30.981 13.069 0.00 1.00 1UBQ
ATOM 229 O ILE X 30 38.544 32.150 12.856 0.00 1.00 1UBQ
ATOM 230 CB ILE X 30 35.708 30.776 13.806 0.00 1.00 1UBQ
ATOM 231 CG1 ILE X 30 34.228 30.630 13.319 0.00 1.00 1UBQ
ATOM 232 CG2 ILE X 30 35.874 32.138 14.512 0.00 1.00 1UBQ
ATOM 233 CD1 ILE X 30 33.284 30.504 14.552 0.00 1.00 1UBQ
ATOM 234 N GLN X 31 38.883 30.110 13.713 0.00 1.00 1UBQ
ATOM 235 CA GLN X 31 40.269 30.508 14.115 0.00 1.00 1UBQ
ATOM 236 C GLN X 31 41.092 30.808 12.851 0.00 1.00 1UBQ
ATOM 237 O GLN X 31 41.828 31.808 12.681 0.00 1.00 1UBQ
ATOM 238 CB GLN X 31 40.996 29.399 14.865 0.00 1.00 1UBQ
ATOM 239 CG GLN X 31 42.445 29.848 15.182 0.00 1.00 1UBQ
ATOM 240 CD GLN X 31 43.090 28.828 16.095 0.00 1.00 1UBQ
ATOM 241 OE1 GLN X 31 42.770 27.655 15.906 0.00 1.00 1UBQ
ATOM 242 NE2 GLN X 31 43.898 29.252 17.050 0.00 1.00 1UBQ
ATOM 243 N ASP X 32 41.001 29.878 11.931 0.00 1.00 1UBQ
ATOM 244 CA ASP X 32 41.718 30.022 10.643 0.00 1.00 1UBQ
ATOM 245 C ASP X 32 41.399 31.338 9.967 0.00 1.00 1UBQ
ATOM 246 O ASP X 32 42.260 32.036 9.381 0.00 1.00 1UBQ
ATOM 247 CB ASP X 32 41.398 28.780 9.810 0.00 1.00 1UBQ
ATOM 248 CG ASP X 32 42.626 28.557 8.928 0.00 1.00 1UBQ
ATOM 249 OD1 ASP X 32 43.666 28.262 9.539 0.00 1.00 1UBQ
ATOM 250 OD2 ASP X 32 42.430 28.812 7.728 0.00 1.00 1UBQ
ATOM 251 N LYS X 33 40.117 31.750 9.988 0.00 1.00 1UBQ
ATOM 252 CA LYS X 33 39.808 32.994 9.233 0.00 1.00 1UBQ
ATOM 253 C LYS X 33 39.837 34.271 9.995 0.00 1.00 1UBQ
ATOM 254 O LYS X 33 40.164 35.323 9.345 0.00 1.00 1UBQ
ATOM 255 CB LYS X 33 38.615 32.801 8.320 0.00 1.00 1UBQ
ATOM 256 CG LYS X 33 37.220 32.822 8.827 0.00 1.00 1UBQ
ATOM 257 CD LYS X 33 36.351 33.613 7.838 0.00 1.00 1UBQ
ATOM 258 CE LYS X 33 36.322 32.944 6.477 0.00 1.00 1UBQ
ATOM 259 NZ LYS X 33 35.768 33.945 5.489 0.00 1.00 1UBQ
ATOM 260 N GLU X 34 39.655 34.335 11.285 0.00 1.00 1UBQ

=== message truncated ===

                
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