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

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

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

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 wrote: > Dear GROMACS users, > > > I used pdb2gmx to generate topology file for the g_quadruplex DNA which >

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

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