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