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

Changdong LIU lcd at ust.hk
Wed May 10 10:16:42 CEST 2017

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"

; 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?




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