[gmx-users] pdb2gmx handle the dna structure containing potassium
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 chain topologies
; Include water topology
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include topology for ions
[ system ]
[ molecules ]
; Compound #mols
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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