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