[gmx-users] Special bonds with terminal residue

[Justin Lemkul]

On 3/7/13 5:44 AM, Baptiste Demoulin wrote:
> Hello Gromacs users,
>
> I try to link a metallic core to its surrounding amino-acids. Everything
> works find for bonding side chains and metal atoms, but I have troubles
> when it comes to bonding COO- group from a terminus ALA. The error printed
> by pdb2gmx is the following :
>
> Program pdb2gmx, VERSION 4.6
> Source code file: /home1/retegan/software/gromacs-4.6/src/kernel/pgutil.c,
> line: 126
>
> Fatal error:
> Residue 334 named ALA of a molecule in the input file was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type special bond in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> Here my specbon.dat file :
>
> 22
> CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
> CYS     SG      1       HEM     FE      2       0.25    CYS2    HEME
> CYS     SG      1       HEM     CAB     1       0.18    CYS2    HEME
> CYS     SG      1       HEM     CAC     1       0.18    CYS2    HEME
> MET     SD      1       HEM     FE      1       0.24    MET     HEME
> CO      C       1       HEME    FE      1       0.19    CO      HEME
> CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
> HIS     NE2     1       FE2     FE      4       0.23    HID     FE2
> HIS     NE2     1       OEX     MN1     6       0.21    HID     OEX
> ASP     OD2     1       OEX     MN1     6       0.23    ASP     OEX
> GLU     OE2     1       OEX     MN1     6       0.20    GLU     OEX
> GLU     OE1     1       OEX     MN2     6       0.21    GLU     OEX
> ASP     OD1     1       OEX     MN2     6       0.21    ASP     OEX
> ALA     OXT     1       OEX     MN2     6       0.20    ALA     OEX
> GLU     OE1     1       OEX     MN3     6       0.21    GLU     OEX
> GLU     OE2     1       OEX     MN3     6       0.23    GLU     OEX
> SOX     O       1       OEX     MN4     6       0.21    SOX     OEX
> ASP     OD2     1       OEX     MN4     6       0.21    ASP     OEX
> GLU     OE2     1       OEX     MN4     6       0.22    GLU     OEX
> SOX     O       1       OEX     CA1     6       0.25    SOX     OEX
> ALA     O       1       OEX     CA1     6       0.25    ALA     OEX
>
> I tried to change the atom names within specbond.dat, in the initial pdb
> file, but nothing has worked yet... Does someone have an idea of what is
> going on ?
>

Terminal oxygens are renamed according to the specifications in the relevant 
.c.tdb file.  A terminal residue has no atom named "O" since the name is 
changed.  If only one bond is missing, it's probably easiest to just manually 
add it to the topology, otherwise remove the offending line in specbond.dat, see 
how the terminal oxygens are renamed, and then try using the relevant atom 
name(s) for creating your bonds.  If that approach doesn't work, then the only 
option is manual addition to the topology.

-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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