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

[Justin Lemkul]

On 5/10/17 4:16 AM, Changdong LIU 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?
>

Make sure you're using a decent force field, e.g. see extensive work by Sponer 
and others about all the nasty defects in existing force fields for GQ 
simulations.  Spoiler alert: none of them do a great job.  But an old AMBER FF 
like AMBER99 is surely a poor choice.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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