[gmx-users] g_x2top help

Justin Lemkul jalemkul at vt.edu
Tue Dec 11 22:59:45 CET 2012



On 12/11/12 4:40 PM, Milinda Samaraweera wrote:
>
>
> Hi Gromacs users
>
> I have a problem Im trying to form a .top file using a g_x2top -f -o -ff command. I have defined .n2t .rtp .itp files. and wanted to construct a topology file. but the script does not identify any of the atoms from .gro file.
>
> my .n2t file
>
> ; clayff
> ; n2t
> H    h*    0.4100     1.008  1    O  0.100             ;water hydrogen
> H    ho    0.4250     1.008  1    O  0.100             ;hydrxyl hydrogen
> O    o*   -0.8200    15.998  2    H  0.100    H  0.100 ;water oxygen
> O    oh   -0.9500    15.998  1    H  0.100             ;hydroxyl oxygen
> O    ob   -1.0500    15.998  0                     ;bridging oxygen
> O  obos   -1.1808    15.998  0                     ;bridging oxygen with octahedral substitution
> O  obts   -1.1688    15.998  0                     ;bridging oxygen with tetrahedral substitution
> O  obss   -1.2996    15.998  0                     ;bridging oxygen with double substitution
> O   ohs   -1.0808    15.998  1      H  0.100       ;hydroxyl hydrogen with substitution
> Si   st    2.1000    28.086  0                     ;tetrahedral silicon
> Al   ao    1.5750    26.982  0                     ;octahedral aluminium
> Al   at    1.5750    26.982  0                     ;tetrahedral aluminium
> Mg  mgo    1.3600    24.305  0                     ; octahedral magnisium
> Na   Na    1.0000    22.999  0                     ;sodium ion
>
> my.itp file
>
> ;
> ;
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               3               yes             0.5     0.5
> ; parameters are taken from the clay force field
>
> [ atomtypes ]
> ; The charges here will be overwritten by those in the rtp file
> ; name       mass      charge    ptype      sigma      eps
>    h*   1      1.00800     0.4100    A    0.00000e-01  0.00000e-01 ;clayFF_waterhydrogen
>    ho   1      1.00800     0.4250    A    0.00000e-01  0.00000e-01 ;clayFF_hydroxylhydrogen
>    o*   8     15.99800    -0.8200    A    3.16557e-01  6.50209e-01 ;ClayFF_wateroxygen
>    oh   8     15.99800    -0.9500    A    3.16557e-01  6.50209e-01 ;ClayFF_hydroxyloxygen
>    ob   8     15.99800    -1.0500    A    3.16557e-01  6.50209e-01 ;ClayFF_bridgingoxygen
>    obos 8     15.99800    -1.1808    A    3.16557e-01  6.50209e-01 ;ClayFF_bridgingoxygenoctasub
>    obts 8     15.99800    -1.1688    A    3.16557e-01  6.50209e-01 ;ClayFF_bridgingoxygentetrsub
>    ohs  8     15.99800    -1.0808    A    3.16557e-01  6.50209e-01 ;ClayFF_hydroxyloxygensub
>    st  14     28.08600     2.1000    A    3.30208e-01  8.0e-06        ;ClayFF_tetrahedralsilicon
>    ao  13     26.98200     1.5750    A    4.27128e-01  6.0e-06     ;ClayFF_octahedalaluminium
>    at  13     26.98200     1.5750    A    3.30206e-01  8.0e-06        ;ClayFF_tetrasubaluminium
>    mgo 12     24.30500     1.3600    A    5.26437e-01  4.0e-06        ;ClayFF_octasubmagnisium
>    Na  11     22.999       1.0000    A    1.89744e-01  6.72427e-01    ;ClayFF_Na
>
> [ bondtypes ]
> ; i    j func        b0          kb
>    oh    ho      1    0.10000   463711.2         ; O-H
>   ohs    ho      1    0.10000   463711.2         ; O-H
>    o*    h*      1    0.10000   463711.2         ; O-H
>
> [ angletypes ]
>    ao     oh     ho      1   109.470    251.046   ; angle Al-O-H
>    mgo    ohs    ho      1   109.470    251.046   ; angle Mg-O-H
>    h*     o*     h*      1   109.470    383.009   ; angle H-O-H
>
> [ dihedraltypes ]
>
> my .gro file
>
> 1Created by VESTA
>   2808
>      Clay    ao    1   0.005   0.564  -0.021
>      Clay    ao    2  -0.602   0.564   3.099
>      Clay    ao    3   4.226   0.564  -0.021
>      Clay    ao    4   3.620   0.564   3.099
>      Clay    st    5   0.178   0.254   0.256
>      Clay    ob    6   0.175   0.240   0.090
>      Clay    ob    7   0.201   0.411   0.296
>      Clay    ob    8   0.037   0.622   0.318
>      Clay    oh    9   0.192  -0.046   0.090
>      Clay    oh   10   0.192   3.610   0.090
>      Clay    ho   11   0.099  -0.046   0.151
>      Clay    ho   12   0.099   3.610   0.151
>      Clay    st   13   0.058   0.254   1.263
>      Clay    ob   14   0.061   0.240   1.429
>      Clay    ob   15   0.035   0.411   1.222
>      Clay    ob   16   0.199   0.622   1.200
>      Clay    oh   17   0.044  -0.046   1.429
>      Clay    oh   18   0.044   3.610   1.429
>      Clay    ho   19   0.136  -0.046   1.368
>      Clay    ho   20   0.136   3.610   1.368
>      Clay    ao   21   0.005   0.259  -0.021
>      Clay    ao   22  -0.602   0.259   3.099
>      Clay    ao   23   4.226   0.259  -0.021
>      Clay    ao   24   3.620   0.259   3.099
>      Clay    st   25   0.058   0.568   1.263
>      Clay    ob   26   0.061   0.582   1.429
>      Clay    ob   27   0.199   0.200   1.200
>      Clay    st   28   0.178   0.568   0.256
>      Clay    ob   29   0.175   0.582   0.090
>      Clay    ob   30   0.037   0.200   0.318
>      Clay    ao   31   0.268   0.107  -0.021
>      Clay    ao   32  -0.338   0.107   3.099
>
> could any one please let me know what might be the problem
>

Well what error do you get?  There are a number of possible issues, but without 
knowing what the problem is, it's all guesswork.  Potential issues:

1. In place of atom names in the .gro file, you're using atom types
2. The .gro file does not have residue numbers anywhere (see 
http://manual.gromacs.org/online/gro.html)

-Justin

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

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

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



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