I have a .gro file and I am trying to convert is to a .top file using x2top. The .gro file is as follows:
Octyl Beta Glucoside 48 1OBG O 1 2.840 2.397 2.515 1OBG C 2 2.938 2.408 2.468 1OBG H 3 2.946 2.418 2.356 1OBG C 4 2.751 2.52 2.465 1OBG H 5 2.725 2.530 2.361 1OBG C 6 3.004 2.528 2.536 1OBG H 7 3.007 2.513 2.647 1OBG C 8 2.778 2.639 2.538 1OBG H 9 2.765 2.632 2.650 1OBG C 10 2.926 2.657 2.503 1OBG H 11 2.938 2.681 2.394 1OBG O 12 2.702 2.747 2.486 1OBG H 13 2.739 2.827 2.525 1OBG O 14 3.136 2.551 2.488 1OBG H 15 3.181 2.465 2.486 1OBG O 16 2.973 2.766 2.581 1OBG H 17 3.068 2.771 2.566 1OBG O 18 2.610 2.480 2.539 1OBG C 19 3.000 2.275 2.513 1OBG H 20 3.019 2.276 2.623 1OBG H 21 2.931 2.190 2.487 1OBG O 22 3.123 2.263 2.443 1OBG H 23 3.156 2.174 2.460 1OBG C 24 2.487 2.516 2.452 1OBG H 25 2.491 2.627 2.440 1OBG H 26 2.491 2.467 2.351 1OBG C 27 2.364 2.472 2.530 1OBG H 28 2.367 2.518 2.632 1OBG H 29 2.366 2.361 2.543 1OBG C 30 2.239 2.515 2.457 1OBG H 31 2.238 2.626 2.445 1OBG H 32 2.238 2.471 2.354 1OBG C 33 2.115 2.470 2.532 1OBG H 34 2.116 2.513 2.636 1OBG H 35 2.115 2.359 2.542 1OBG C 36 1.989 2.515 2.461 1OBG H 37 1.988 2.626 2.452 1OBG H 38 1.988 2.473 2.357 1OBG C 39 1.865 2.469 2.535 1OBG H 40 1.866 2.509 2.639 1OBG H 41 1.865 2.357 2.543 1OBG C 42 1.739 2.514 2.465 1OBG H 43 1.739 2.626 2.457 1OBG H 44 1.738 2.474 2.360 1OBG C 45 1.615 2.468 2.537 1OBG H 46 1.613 2.509 2.642 1OBG H 47 1.612 2.357 2.543 1OBG H 48 1.608 2.410 2.453 2.00000 2.00000 2.00000 I have tried to convert this file to a top file but this is the error message I get: Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 48 Can not find forcefield for atom C-4 with 2 bonds ------------------------------------------------------- Program x2top, VERSION 4.0.7 Source code file: ../../../../src/kernel/x2top.c, line: 207 Fatal error: Could only find a forcefield type for 47 out of 48 atoms ------------------------------------------------------- "Throwing the Baby Away With the SPC" (S. Hayward) I have tried to adjust the coordinates within the gro file but it still shows the same message. Someone please give me some proper instruction in the conversion of a .gro file to a .top file. Thank you! Sincerely, Amanda M. Watkins SBC 2012
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