[gmx-users] Errors pdb2gmx

[Stefania Evoli]

Hi everybody,

I’m simulating for the first time the riboswitch in presence of metals, usually I work only with proteins. I modified the pdb file to have the 5’ and 3’ terminals but when I try to use pdb2gmx_mpi_d (Gromacs 5.0.5) to generate gro and top file with the ff amber99sb-ildn I get the error 'Residue 'F' not found in residue topology database’. I checked in the atomtype database fluorine is called with ‘F’. I don’t understand what I’m doing wrong. Could someone help me, please?

The last part of my pdb file is like


ATOM   1109  N1    G A  52       5.885  15.987 -29.904  1.00106.05           N

ATOM   1110  C2    G A  52       6.739  16.703 -29.104  1.00108.63           C

ATOM   1111  N2    G A  52       7.547  17.572 -29.727  1.00108.84           N

ATOM   1112  N3    G A  52       6.796  16.580 -27.788  1.00112.10           N

ATOM   1113  C4    G A  52       5.924  15.660 -27.307  1.00113.15           C

TER    1114        G A  52

HETATM 1115 MG    MG A 101     -12.105  14.253 -12.775  1.00 42.94          MG

HETATM 1116 MG    MG A 102      -1.621  16.836 -16.694  1.00 57.68          MG

HETATM 1117 MG    MG A 103     -10.729  16.277 -10.240  1.00 54.29          MG

HETATM 1118 MG    MG A 104     -13.066  14.112 -10.060  1.00 38.13          MG

HETATM 1119 MG    MG A 105      10.592  16.076 -23.407  1.00114.31          MG

HETATM 1120  F     F A 106     -11.635  14.767 -10.999  1.00 37.49           F

HETATM 1121  K     K A 107     -15.304  15.848 -12.170  1.00 75.41           K

HETATM 1122  O   HOH A 201      -3.046  15.371 -17.019  1.00 60.47           O

HETATM 1123  O   HOH A 202      -9.781  18.114  -9.629  1.00 39.40           O

HETATM 1124  O   HOH A 203     -10.387  15.232 -13.471  1.00 40.03           O

HETATM 1125  O   HOH A 204     -13.816  13.609 -11.929  1.00 36.59           O

HETATM 1126  O   HOH A 205     -11.326  12.355 -12.487  1.00 41.22           O

HETATM 1127  O   HOH A 206     -16.414  13.856 -13.423  1.00 46.60           O

HETATM 1128  O   HOH A 207     -14.624  13.020  -9.235  1.00 48.49           O

HETATM 1129  O   HOH A 208     -12.325  12.095 -10.081  1.00 42.16           O

HETATM 1130  O   HOH A 209      -2.988  18.280 -16.047  1.00 46.13           O

HETATM 1131  O   HOH A 210      -0.566  15.325 -17.495  1.00 50.52           O

HETATM 1132  O   HOH A 211      -1.864  17.062 -18.764  1.00 53.50           O

HETATM 1133  O   HOH A 212      -7.387  18.633 -10.494  1.00 40.88           O

HETATM 1134  O   HOH A 213     -10.571   9.493 -10.828  1.00 52.53           O

HETATM 1135  O   HOH A 214      -3.704  27.050  -9.237  1.00 60.38           O

HETATM 1136  O   HOH A 215     -11.800  42.303 -11.267  1.00 59.89           O

HETATM 1137  O   HOH A 216     -10.633  32.221 -20.335  1.00 79.49           O

HETATM 1138  O   HOH A 217      -0.062   4.774  -3.205  1.00 88.09           O

HETATM 1139  O   HOH A 218     -25.127  -9.600   1.612  1.00 71.27           O

HETATM 1140  O   HOH A 219     -16.317  25.773  -3.277  1.00 85.21           O

HETATM 1141  O   HOH A 220     -19.507  19.430  -0.328  1.00 87.20           O

HETATM 1142  O   HOH A 221     -33.017  10.031  -0.836  1.00 72.84           O


I also tried to use ‘TER’ at the end of each ion (in previous Gromacs version it worked) but I didn’t solve the problem.

Thank you,

Stefania


—
Dr. Stefania Evoli
Post-Doctoral Fellow
King Abdullah University of Science and Technology
Catalysis center - Bldg. 3, 4th floor, 4231–WS18
Thuwal, Kingdom of Saudi Arabia
stefania.evoli at kaust.edu.sa



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