# Re: pair.pdb and cutoff for pairInteraction

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Nov 30 2005 - 00:10:44 CST

I should correct myself; the magnitude of the force will always be
positive. You won't always see an opposite correlation between the
signs of the potential (which can be shifted anyway based on a
different "zero point") and the force (which is a vector anyway).

Sorry if I made things murkier for you. I can clarify more later if
necessary.

On Nov 30, 2005, at 12:52 AM, JC Gumbart wrote:

> 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 - 15:41:24 CST