[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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