[gmx-users] Using x2top to convert a gro file to a top file
Amanda Watkins
mhstrumpetgirl at yahoo.com
Wed Jun 30 21:10:43 CEST 2010
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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