[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 <jalemkul at vt.edu>

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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