Re: [gmx-users] Special bonds with terminal residue

[Baptiste Demoulin]

Thank you for your answer.

I had tried to change the names before, but the error was then that the
atoms were not recognized. Reading your answer made me realize that I had
not gone far enough,

The solution I found is to create a residue in the .rtp that has the same
features as the terminal AA, but with a different name. Then, the fragment
is renamed in the .pdb file according to this new residue (the atoms are
renamed to), end the "TER" line is removed. I also added a block in .hdb
file. And now it works well !

Thank you again !

Baptiste


2013/3/7 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 CYS2CYS2
>> CYS SG  1   HEM FE  2   0.25CYS2HEME
>> CYS SG  1   HEM CAB 1   0.18CYS2HEME
>> CYS SG  1   HEM CAC 1   0.18CYS2HEME
>> MET SD  1   HEM FE  1   0.24MET HEME
>> CO  C   1   HEMEFE  1   0.19CO  HEME
>> CYM SG  1   CYM SG  1   0.2 CYS2CYS2
>> HIS NE2 1   FE2 FE  4   0.23HID FE2
>> HIS NE2 1   OEX MN1 6   0.21HID OEX
>> ASP OD2 1   OEX MN1 6   0.23ASP OEX
>> GLU OE2 1   OEX MN1 6   0.20GLU OEX
>> GLU OE1 1   OEX MN2 6   0.21GLU OEX
>> ASP OD1 1   OEX MN2 6   0.21ASP OEX
>> ALA OXT 1   OEX MN2 6   0.20ALA OEX
>> GLU OE1 1   OEX MN3 6   0.21GLU OEX
>> GLU OE2 1   OEX MN3 6   0.23GLU OEX
>> SOX O   1   OEX MN4 6   0.21SOX OEX
>> ASP OD2 1   OEX MN4 6   0.21ASP OEX
>> GLU OE2 1   OEX MN4 6   0.22GLU OEX
>> SOX O   1   OEX CA1 6   0.25SOX OEX
>> ALA O   1   OEX CA1 6   0.25ALA 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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Re: [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 CYS2CYS2
CYS SG  1   HEM FE  2   0.25CYS2HEME
CYS SG  1   HEM CAB 1   0.18CYS2HEME
CYS SG  1   HEM CAC 1   0.18CYS2HEME
MET SD  1   HEM FE  1   0.24MET HEME
CO  C   1   HEMEFE  1   0.19CO  HEME
CYM SG  1   CYM SG  1   0.2 CYS2CYS2
HIS NE2 1   FE2 FE  4   0.23HID FE2
HIS NE2 1   OEX MN1 6   0.21HID OEX
ASP OD2 1   OEX MN1 6   0.23ASP OEX
GLU OE2 1   OEX MN1 6   0.20GLU OEX
GLU OE1 1   OEX MN2 6   0.21GLU OEX
ASP OD1 1   OEX MN2 6   0.21ASP OEX
ALA OXT 1   OEX MN2 6   0.20ALA OEX
GLU OE1 1   OEX MN3 6   0.21GLU OEX
GLU OE2 1   OEX MN3 6   0.23GLU OEX
SOX O   1   OEX MN4 6   0.21SOX OEX
ASP OD2 1   OEX MN4 6   0.21ASP OEX
GLU OE2 1   OEX MN4 6   0.22GLU OEX
SOX O   1   OEX CA1 6   0.25SOX OEX
ALA O   1   OEX CA1 6   0.25ALA 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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