[gmx-users] pdb2gmx handle the dna structure containing potassium

[Tasneem Kausar]

Take a look at you pdb file. May be potassium atom is defined as HETATM in
pdb. amber99sb-ildn ff has K in its ions.itp file.

On Wed, May 10, 2017 at 1:46 PM, Changdong LIU <lcd at ust.hk> wrote:

> Dear GROMACS users,
>
>
>  I used pdb2gmx to generate topology file for the g_quadruplex DNA which
> constains 3 potassiums.
>
>
>  If the 3 potassiums were deleted ,the pdb2gma successfully generated the
> topology file for DNA.
>
>
> But failed when the 3 potassiums were added into the pdb file. The
> topol.top is like:
>
>
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_DNA_chain_C.itp"
> #include "topol_Ion_chain_D.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> ---
>
> [ molecules ]
> ; Compound        #mols
> DNA_chain_C         1
> Ion_chain_D         1
>
>
> It seems that pdb2gmx could not recognize both dna and potassiums.
>
> As the potassium is necessary for the stability of the DNA g_quadruplex,
> would you please give any suggestions how to generated the topology file
> containing the ions?
>
> Thanks.
>
>
> Best
>
> Changdong
>
>
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