[gmx-users] pdb2gmx handle the dna structure containing potassium
jalemkul at vt.edu
Wed May 10 19:46:16 CEST 2017
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
> ; 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 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
More information about the gromacs.org_gmx-users