[gmx-users] problems with my PDB file
Joshua Adelman
jadelman at berkeley.edu
Sat Apr 4 20:17:34 CEST 2009
Hi Jacob,
It looks like your pdb file does not contain any residue names, since
you residue column is filled with the number "2" which I'm guessing
isn't specified as a canonical residue. I'm not sure how you're
generating this PDB file, but if you're doing it by hand, I would
strongly recommend consulting the pdb formatting guide.
Josh
On Apr 4, 2009, at 11:03 AM, Jacob Harvey wrote:
> 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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------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman at berkeley.edu
------------------------------------------------------------------------------------------------------
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