# Re: pair.pdb and cutoff for pairInteraction

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Nov 29 2005 - 23:52:51 CST

The force is always the negative gradient of the potential energy (F =
- grad U, for conservative forces which we are dealing with here). So
for both, the sign of the magnitudes will be opposite (for VDW and
electrostatics).

You are also right that positive force means repulsion and negative
means attraction.

On Nov 29, 2005, at 11:33 PM, Shirley Li wrote:

> 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 ===
> Yahoo! Music Unlimited - Access over 1 million songs. Try it free.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:10 CST