[gmx-users] error message
Maria Sabaye Moghaddam
msabaye at gibbs.med.utoronto.ca
Tue Sep 21 16:37:40 CEST 2004
An embedded message was scrubbed...
From: unknown sender
Subject: no subject
Date: no date
Size: 18146
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040921/fbb1a166/attachment.mht>
-------------- next part --------------
Thanks a lot Hector. I actually had to change
both the box size and rcoulomb to do away
with that error message.
Thanks Again,
Maria.
Quoting Hector Martinez-Seara Monne <h.seara at qf.ub.es>:
> Maria Sabaye Moghaddam wrote:
>
> >Thanks a lot. I am looking at *.gro file and I cannot find where
> >the box size is located. Are the 3 numbers at the end? I will
> >attach the file if you don't mind.
> >
> >Thanks Again,
> >Maria.
> >
> >
> >
> >On Mon, 20 Sep 2004, Hector Martinez-Seara Monne wrote:
> >
> >
> > [NON-Text Body part not included]
> >
> >
> >------------------------------------------------------------------------
> >
> >GROningen MAchine for Chemical Simulation
> > 202
> > 1SER N 1 1.277 1.253 -0.210
> > 1SER H1 2 1.343 1.209 -0.270
> > 1SER H2 3 1.214 1.185 -0.174
> > 1SER H3 4 1.225 1.321 -0.263
> > 1SER CA 5 1.346 1.319 -0.101
> > 1SER CB 6 1.439 1.427 -0.153
> > 1SER OG 7 1.371 1.513 -0.243
> > 1SER HG 8 1.434 1.583 -0.277
> > 1SER C 9 1.239 1.382 -0.017
> > 1SER O 10 1.244 1.378 0.105
> > 2ILE N 11 1.139 1.439 -0.084
> > 2ILE H 12 1.137 1.436 -0.184
> > 2ILE CA 13 1.033 1.507 -0.012
> > 2ILE CB 14 0.947 1.600 -0.100
> > 2ILE CG1 15 1.032 1.669 -0.207
> > 2ILE CG2 16 0.881 1.709 -0.015
> > 2ILE CD 17 0.986 1.811 -0.235
> > 2ILE C 18 0.952 1.414 0.078
> > 2ILE O 19 0.909 1.455 0.188
> > 3ARG N 20 0.934 1.289 0.036
> > 3ARG H 21 0.972 1.262 -0.053
> > 3ARG CA 22 0.861 1.190 0.116
> > 3ARG CB 23 0.822 1.067 0.032
> > 3ARG CG 24 0.676 1.069 -0.022
> > 3ARG CD 25 0.651 0.961 -0.130
> > 3ARG NE 26 0.618 1.018 -0.261
> > 3ARG HE 27 0.609 1.118 -0.266
> > 3ARG CZ 28 0.600 0.948 -0.373
> > 3ARG NH1 29 0.612 0.816 -0.371
> > 3ARG HH11 30 0.634 0.786 -0.278
> > 3ARG HH12 31 0.595 0.780 -0.463
> > 3ARG NH2 32 0.571 1.011 -0.487
> > 3ARG HH21 33 0.567 1.109 -0.471
> > 3ARG HH22 34 0.561 0.943 -0.560
> > 3ARG C 35 0.942 1.148 0.241
> > 3ARG O 36 0.886 1.117 0.347
> > 4GLU N 37 1.075 1.148 0.231
> > 4GLU H 38 1.120 1.171 0.146
> > 4GLU CA 39 1.151 1.113 0.351
> > 4GLU CB 40 1.295 1.066 0.322
> > 4GLU CG 41 1.357 0.990 0.445
> > 4GLU CD 42 1.260 0.891 0.507
> > 4GLU OE1 43 1.181 0.835 0.429
> > 4GLU OE2 44 1.261 0.870 0.630
> > 4GLU C 45 1.150 1.227 0.453
> > 4GLU O 46 1.147 1.202 0.574
> > 5LEU N 47 1.152 1.351 0.402
> > 5LEU H 48 1.157 1.362 0.303
> > 5LEU CA 49 1.147 1.473 0.486
> > 5LEU CB 50 1.163 1.599 0.401
> > 5LEU CG 51 1.281 1.590 0.306
> > 5LEU CD1 52 1.278 1.699 0.199
> > 5LEU CD2 53 1.406 1.597 0.387
> > 5LEU C 54 1.011 1.478 0.557
> > 5LEU O 55 1.005 1.502 0.676
> > 6GLU N 56 0.903 1.454 0.482
> > 6GLU H 57 0.914 1.441 0.384
> > 6GLU CA 58 0.767 1.448 0.540
> > 6GLU CB 59 0.670 1.406 0.430
> > 6GLU CG 60 0.524 1.450 0.442
> > 6GLU CD 61 0.444 1.416 0.315
> > 6GLU OE1 62 0.404 1.510 0.243
> > 6GLU OE2 63 0.424 1.295 0.287
> > 6GLU C 64 0.762 1.347 0.657
> > 6GLU O 65 0.718 1.379 0.769
> > 7ALA N 66 0.815 1.228 0.634
> > 7ALA H 67 0.851 1.207 0.543
> > 7ALA CA 68 0.822 1.128 0.739
> > 7ALA CB 69 0.883 0.999 0.687
> > 7ALA C 70 0.900 1.176 0.861
> > 7ALA O 71 0.860 1.151 0.975
> > 8ARG N 72 1.012 1.245 0.839
> > 8ARG H 73 1.041 1.264 0.745
> > 8ARG CA 74 1.093 1.292 0.951
> > 8ARG CB 75 1.231 1.338 0.904
> > 8ARG CG 76 1.328 1.225 0.868
> > 8ARG CD 77 1.445 1.289 0.795
> > 8ARG NE 78 1.548 1.343 0.887
> > 8ARG HE 79 1.531 1.339 0.985
> > 8ARG CZ 80 1.664 1.397 0.845
> > 8ARG NH1 81 1.690 1.407 0.716
> > 8ARG HH11 82 1.613 1.370 0.663
> > 8ARG HH12 83 1.780 1.449 0.703
> > 8ARG NH2 84 1.755 1.439 0.933
> > 8ARG HH21 85 1.721 1.423 1.026
> > 8ARG HH22 86 1.834 1.476 0.884
> > 8ARG C 87 1.020 1.401 1.033
> > 8ARG O 88 1.020 1.398 1.156
> > 9ILE N 89 0.956 1.494 0.964
> > 9ILE H 90 0.959 1.495 0.864
> > 9ILE CA 91 0.879 1.595 1.037
> > 9ILE CB 92 0.823 1.697 0.933
> > 9ILE CG1 93 0.934 1.783 0.875
> > 9ILE CG2 94 0.731 1.796 1.001
> > 9ILE CD 95 0.885 1.875 0.763
> > 9ILE C 96 0.760 1.526 1.113
> > 9ILE O 97 0.736 1.553 1.227
> > 10ARG N 98 0.684 1.438 1.050
> > 10ARG H 99 0.702 1.416 0.954
> > 10ARG CA 100 0.574 1.372 1.122
> > 10ARG CB 101 0.519 1.266 1.029
> > 10ARG CG 102 0.402 1.194 1.083
> > 10ARG CD 103 0.354 1.106 0.974
> > 10ARG NE 104 0.465 1.031 0.916
> > 10ARG HE 105 0.518 0.973 0.977
> > 10ARG CZ 106 0.500 1.034 0.788
> > 10ARG NH1 107 0.433 1.109 0.701
> > 10ARG HH11 108 0.359 1.157 0.748
> > 10ARG HH12 109 0.474 1.099 0.610
> > 10ARG NH2 110 0.601 0.960 0.746
> > 10ARG HH21 111 0.638 0.908 0.822
> > 10ARG HH22 112 0.614 0.974 0.648
> > 10ARG C 113 0.615 1.312 1.254
> > 10ARG O 114 0.550 1.329 1.358
> > 11GLU N 115 0.728 1.243 1.256
> > 11GLU H 116 0.781 1.232 1.172
> > 11GLU CA 117 0.775 1.185 1.381
> > 11GLU CB 118 0.898 1.102 1.348
> > 11GLU CG 119 0.878 1.035 1.217
> > 11GLU CD 120 0.984 0.929 1.189
> > 11GLU OE1 121 1.055 0.894 1.285
> > 11GLU OE2 122 0.993 0.883 1.073
> > 11GLU C 123 0.816 1.284 1.485
> > 11GLU O 124 0.798 1.263 1.604
> > 12LEU N 125 0.875 1.394 1.440
> > 12LEU H 126 0.890 1.404 1.341
> > 12LEU CA 127 0.920 1.499 1.531
> > 12LEU CB 128 0.991 1.612 1.453
> > 12LEU CG 129 1.144 1.604 1.431
> > 12LEU CD1 130 1.189 1.708 1.326
> > 12LEU CD2 131 1.215 1.627 1.565
> > 12LEU C 132 0.797 1.557 1.600
> > 12LEU O 133 0.796 1.579 1.723
> > 13GLU N 134 0.696 1.579 1.518
> > 13GLU H 135 0.708 1.558 1.421
> > 13GLU CA 136 0.567 1.634 1.559
> > 13GLU CB 137 0.472 1.642 1.439
> > 13GLU CG 138 0.468 1.775 1.372
> > 13GLU CD 139 0.419 1.769 1.231
> > 13GLU OE1 140 0.379 1.660 1.187
> > 13GLU OE2 141 0.419 1.875 1.164
> > 13GLU C 142 0.509 1.540 1.661
> > 13GLU O 143 0.469 1.580 1.770
> > 14LEU N 144 0.505 1.413 1.623
> > 14LEU H 145 0.538 1.389 1.532
> > 14LEU CA 146 0.452 1.307 1.709
> > 14LEU CB 147 0.459 1.172 1.636
> > 14LEU CG 148 0.333 1.152 1.549
> > 14LEU CD1 149 0.348 1.046 1.439
> > 14LEU CD2 150 0.221 1.120 1.641
> > 14LEU C 151 0.520 1.307 1.847
> > 14LEU O 152 0.452 1.319 1.951
> > 15ARG N 153 0.654 1.300 1.845
> > 15ARG H 154 0.699 1.292 1.756
> > 15ARG CA 155 0.739 1.304 1.965
> > 15ARG CB 156 0.888 1.304 1.925
> > 15ARG CG 157 0.945 1.168 1.884
> > 15ARG CD 158 1.094 1.176 1.849
> > 15ARG NE 159 1.126 1.113 1.720
> > 15ARG HE 160 1.054 1.059 1.676
> > 15ARG CZ 161 1.243 1.124 1.658
> > 15ARG NH1 162 1.342 1.195 1.712
> > 15ARG HH11 163 1.312 1.234 1.799
> > 15ARG HH12 164 1.422 1.192 1.652
> > 15ARG NH2 165 1.262 1.064 1.541
> > 15ARG HH21 166 1.178 1.016 1.515
> > 15ARG HH22 167 1.354 1.082 1.508
> > 15ARG C 168 0.713 1.430 2.048
> > 15ARG O 169 0.677 1.423 2.166
> > 16ILE N 170 0.734 1.545 1.984
> > 16ILE H 171 0.763 1.542 1.889
> > 16ILE CA 172 0.715 1.674 2.047
> > 16ILE CB 173 0.748 1.784 1.949
> > 16ILE CG1 174 0.899 1.809 1.949
> > 16ILE CG2 175 0.673 1.913 1.980
> > 16ILE CD 176 0.938 1.928 1.864
> > 16ILE C 177 0.572 1.689 2.095
> > 16ILE O1 178 0.488 1.585 2.072
> > 16ILE O2 179 0.540 1.806 2.157
> > 17NA NA 180 1.114 0.643 0.534
> > 18ZN ZN 181 1.114 0.643 1.164
> > 19HOH OW 182 1.114 0.643 0.863
> > 19HOH HW1 183 1.195 0.643 0.921
> > 19HOH HW2 184 1.032 0.643 0.921
> > 20HOH OW 185 -0.000 1.286 1.210
> > 20HOH HW1 186 0.082 1.286 1.268
> > 20HOH HW2 187 0.000 1.368 1.152
> > 21HOH OW 188 0.239 1.463 1.281
> > 21HOH HW1 189 0.320 1.463 1.338
> > 21HOH HW2 190 0.239 1.382 1.223
> > 22HOH OW 191 0.473 2.117 1.270
> > 22HOH HW1 192 0.391 2.117 1.328
> > 22HOH HW2 193 0.473 2.199 1.213
> > 23HOH OW 194 0.583 1.062 0.423
> > 23HOH HW1 195 0.501 1.062 0.481
> > 23HOH HW2 196 0.583 0.980 0.366
> > 24HOH OW 197 1.171 0.933 0.887
> > 24HOH HW1 198 1.171 1.014 0.830
> > 24HOH HW2 199 1.171 0.851 0.830
> > 25HOH OW 200 0.726 0.878 1.020
> > 25HOH HW1 201 0.808 0.878 1.078
> > 25HOH HW2 202 0.645 0.878 1.078
> > 1.83375 1.55605 2.72560
> >
> >
> >
> >
> Yes, those three numbers are the box sizes and they are too small try
> to change them to (5 5 5) and run again. I don't know if you are trying
> to keep these sizes for any special porpouse but if not just do that.
>
> Hector Martínez-Seara Monné
>
> Universidad de Barcelona
>
> Dept. Química Fisica
>
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >
>
>
-------------------------------------------------
This mail sent through IMP: http://horde.org/imp/
More information about the gromacs.org_gmx-users
mailing list