[gmx-users] Special bonds with terminal residue

[Baptiste Demoulin]

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 ?

Thank you very much !

Baptiste