[gmx-users] problems with my PDB file
Jacob Harvey
j.harv8 at gmail.com
Sat Apr 4 20:03:17 CEST 2009
Dear All,
I seem to be having issues with the pdb file I wish to use in gromacs. I am
trying to model this system using the OPLS-AA force field however I get the
error
"Fatal error:
Residue '' not found in residue topology database"
I know what this error means but its not naming a specific residue so I'm
not sure where I am going wrong in terms of naming my atoms. Does anyone see
a way to fix this problem. Thank you.
my pdb file:
HETATM 1 CA 2 2 -4.438 3.334 2.988
HETATM 2 CA 2 2 0.588 3.313 0.517
HETATM 3 CA 2 2 5.476 3.310 -2.216
HETATM 4 H4 2 2 -4.134 2.590 3.731
HETATM 5 H5 2 2 -5.525 3.438 3.047
HETATM 6 H6 2 2 -3.996 4.291 3.276
HETATM 7 H7 2 2 1.480 3.111 1.117
HETATM 8 H8 2 2 -0.266 3.349 1.200
HETATM 9 H9 2 2 0.702 4.307 0.076
HETATM 10 H10 2 2 6.375 3.525 -1.633
HETATM 11 H11 2 2 4.648 3.862 -1.761
HETATM 12 H12 2 2 5.628 3.709 -3.223
HETATM 13 CA 2 2 -3.996 2.922 1.581
HETATM 14 H14 2 2 -2.902 2.862 1.545
HETATM 15 H15 2 2 -4.281 3.703 0.865
HETATM 16 CA 2 2 0.394 2.242 -0.557
HETATM 17 H17 2 2 -0.485 2.486 -1.167
HETATM 18 H18 2 2 1.250 2.252 -1.242
HETATM 19 CA 2 2 5.188 1.805 -2.247
HETATM 20 H20 2 2 6.018 1.286 -2.742
HETATM 21 H21 2 2 4.300 1.615 -2.864
HETATM 22 CA 2 2 -4.587 1.582 1.127
HETATM 23 H23 2 2 -5.682 1.638 1.161
HETATM 24 H24 2 2 -4.298 0.792 1.828
HETATM 25 CA 2 2 0.235 0.836 0.028
HETATM 26 H26 2 2 -0.616 0.818 0.720
HETATM 27 H27 2 2 1.117 0.581 0.625
HETATM 28 CA 2 2 4.981 1.206 -0.852
HETATM 29 H29 2 2 4.152 1.720 -0.350
HETATM 30 H30 2 2 5.867 1.381 -0.234
HETATM 31 CB 2 2 -4.129 1.184 -0.291
HETATM 32 H32 2 2 -4.398 1.981 -0.995
HETATM 33 H33 2 2 -3.041 1.101 -0.315
HETATM 34 CB 2 2 0.034 -0.248 -1.048
HETATM 35 H35 2 2 -0.851 -0.016 -1.650
HETATM 36 H36 2 2 0.890 -0.242 -1.730
HETATM 37 CB 2 2 4.702 -0.306 -0.866
HETATM 38 H38 2 2 3.772 -0.519 -1.404
HETATM 39 H39 2 2 5.504 -0.809 -1.420
HETATM 40 CD2 2 2 -6.169 -1.597 -1.527
HETATM 41 H41 2 2 -6.700 0.434 -1.148
HETATM 42 CE1 2 2 -4.945 -2.182 -1.371
HETATM 43 H43 2 2 -7.118 -1.976 -1.868
HETATM 44 H44 2 2 -4.663 -3.203 -1.569
HETATM 45 CD2 2 2 -1.054 -3.462 0.297
HETATM 46 H46 2 2 -2.230 -1.848 -0.502
HETATM 47 CE1 2 2 0.307 -3.542 0.421
HETATM 48 H48 2 2 -1.844 -4.148 0.553
HETATM 49 H49 2 2 0.898 -4.352 0.820
HETATM 50 CD2 2 2 3.845 -1.970 2.274
HETATM 51 H51 2 2 2.694 -1.850 0.476
HETATM 52 CE1 2 2 5.086 -1.451 2.534
HETATM 53 H53 2 2 3.156 -2.545 2.870
HETATM 54 H54 2 2 5.660 -1.519 3.446
HETATM 55 CG 2 2 -4.687 -0.117 -0.776
HETATM 56 CG 2 2 -0.105 -1.625 -0.478
HETATM 57 CG 2 2 4.625 -0.891 0.514
HETATM 58 NE2 2 2 -5.991 -0.283 -1.145
HETATM 59 ND1 2 2 -4.033 -1.258 -0.903
HETATM 60 NE2 2 2 -1.303 -2.236 -0.278
HETATM 61 ND1 2 2 0.892 -2.392 -0.062
HETATM 62 NE2 2 2 3.558 -1.605 0.977
HETATM 63 ND1 2 2 5.566 -0.779 1.434
--
--
Jacob Harvey
Graduate Student
University of Massachusetts Amherst
j.harv8 at gmail.com
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