[gmx-users] Using x2top to convert a gro file to a top file

[Justin A. Lemkul]

Amanda Watkins wrote:
> 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!
> 

Instead of adjusting the coordinates, you probably need to create a proper .n2t 
entry for this atom type.

http://www.gromacs.org/Documentation/File_Formats/.n2t_File

-Justin

> Sincerely,
> 
> Amanda M. Watkins
> 
> SBC 2012
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================