[gmx-users] specbond recognised but not built

[Tsjerk Wassenaar]

Hi Grange,

It recognizes the possibility of having a bond between these atoms.
That's where the distance matrix comes in. But if a bond were made,
you'd have a statement right after the distance matrix saying
something like "linking atom ... and atom ...". It doesn't happen, and
the reason is the following (you might want to search "specbond" in
the user list archives): You have set your distance at 0.2 nm. pdb2gmx
checks whether the actual distance is within 10% of the distance
specified. The actual distance is 0.134, which lies well under the
target distance. Therefore it doesn't make the bond. Try to set the
bond length in specbond.dat between 0.13 and 0.14.

Hope it helps,

Tsjerk

On Sun, Jun 29, 2008 at 9:20 AM, Grange Hermitage <ghermitage at y7mail.com> wrote:
> Hi all,
>
> I am using gromacs 3.3.3, and have a specbond definition:
> CHU     C3      2       CHV     C4      2       0.2     CHU     CHV
> This is recognised but not built:
> 7 out of 7 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                     CHU5
>                     C341
>     CHV9    C472   0.134
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 13 residues with 123 atoms
> Making bonds...
> Opening library file /home/users/ghermitage/gromacs/3.3.3/top/aminoacids.dat
> Number of bonds was 121, now 121
>
> .top:
> [ atoms ]
> 48        CH1      5    CHU     C3     24          0     13.019   ; qtot
> -1.008
> 83        CH1      9    CHV     C4     42          0     13.019   ; qtot
> -2.016
>
> Indeed, the bond is not built. No bond connecting the two atoms appears in [
> bonds ]
>
> What to do?
> Thanks.
>
>
> From ffgmx.rtp:
> [ CHU ]
> [ atoms ]
>    O         O       -0.669   1
>    C         C        0.380   1
>    CA        CH1      0.169   1
>    N         NL       0.681   1
>    H         H        0.004   1
>    CB        CH2      0.299   1
>    OG        OA      -0.171   1
>    C1        CH2      0.299   1
>    C3        CH1      0.000   2
> [ bonds ]
>  C     O
>  CA    C
>  CA    N
>  CA    CB
>  N     H
>  CB    OG
>  C1    OG
>  C1    C3
> [ CHV ]
> [ atoms ]
>    O         O      -0.669   1
>    C         C       0.380   1
>    CA        CH1     0.169   1
>    N         NL      0.681   1
>    H         H       0.004   1
>    CB        CH2     0.299   1
>    OG        OA     -0.171   1
>    C2        CH2     0..299   1
>    C4        CH1     0.000   2
> [ bonds ]
>    C     O
>    CA    C
>    CA    N
>    CA    CB
>    N     H
>    CB    OG
>    C2    OG
>    C2    C4
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623