[gmx-users] .top file incoherent with the values in the ffbonded.itp file

[Justin A. Lemkul]

On 6/29/12 3:55 PM, sreeta.g wrote:
> Hello
> My A.gro file is:
>   1PvB     CB    1   3.109   2.784   0.803  0.0000  0.0000  0.0000
>      1PvB    HB1    2   3.156   2.880   0.843  0.0000  0.0000  0.0000
>      1PvB    HB2    3   2.997   2.797   0.819  0.0000  0.0000  0.0000
>      1PvB    HB3    4   3.129   2.765   0.693  0.0000  0.0000  0.0000
>      1PvB     CA    5   3.173   2.673   0.879  0.0000  0.0000  0.0000
> ........... (contd.)
>
> My ffbonded.itp file has:
> [ bondtypes ]
> ;   i    j   func   b0(bond length)  kb (force const)
>     CB    HB1  1    0.11       284512
>     CB    HB2  1    0.11       284512
>     CB    HB3  1    0.11       284512.0
> ... (contd)
>
> [ angletypes ]
> ;  i     j    k   func     th0    cth
>    HO    OH   CA    1       105    320
>    CA    CB   CA    1       109.45 482.3
>    CB    CA   CB    1       109.45 482.3
>    OH    CA   CB    1       107.8  460
> ....... (contd)
>
> [ dihedraltypes ]
> ;  i    j    k    l   func    RB coefficients
>     OH  OH   CA   CB        3     3.00000    9.00000 0.00000   -12.00000
> 0.00000   0.0000 ;
>     CA  CB   CA   CB        3     5.75000   17.25000 0.00000   -23.00000
> 0.00000   0.0000 ;
> ..... (contd)
>
> However, my topol.top file looks like this:
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>      1     2     1
>      1     3     1
>      1     4     1
>      1     5     1
>      1    12     1
> ........(contd)
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2
> c3
>      2     1     3     1
>      2     1     4     1
>      2     1     5     1
>      2     1    12     1
>      3     1     4     1
>      3     1     5     1
> ......... (contd)
>
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2
> c3            c4            c5
>      2     1     5     6     3
>      2     1     5     7     3
>      3     1     5     6     3
>      3     1     5     7     3
>      4     1     5     6     3
>      4     1     5     7     3
> ....... (contd)
>
> I have two issues:
> 1) I have mentioned the bond lengths and bond constants in the [bondtypes]
> and [angletypes ]directory of the ffbonded.itp file, however in the [bonds]
> [ angles ]directory in the topol.top file the Ryckaert-Bellemans
> coefficients are used, which are assigned as blanks. This is giving the
> error No default Ryckaert-Bell. types (multiple times).

The "blanks" in the topology are totally normal.  When assembling the .tpr file, 
grompp will look up the appropriate values in ffbonded.itp that match with the 
atom types it finds.  If you are getting errors about missing parameters, you 
have failed to assign some interaction type.  The error message should contain 
the offending lines.  Note, too, that the parameters specified in ffbonded.itp 
are assigned by atom *type* and not atom *name* - perhaps this is the origin of 
your problem.

> 2) Also, the RB coefficients mentioned in the [dihedraltypes] of the
> ffbonded.itp are not used in the [dihedrals] directory of the topol.top
> file. This is again writing blanks for the RB coefficients.
> What is the issue and why is my topl.top file inconsistent with the inputs
> given in the ffbonded.itp file?

The blanks are normal; see above comments.

-Justin

-- 
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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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