Re: [gmx-users] metal_ligand complex

2012-12-04 Thread Justin Lemkul
On 12/3/12 11:55 PM, tarak karmakar wrote: Thanks Justin Yah! We can run steered MD or Umbrella Pulling ( sampling) for this purpose. But one thing I am wondering that how to move the entire complex. In my model there are no covalent bond ( bonding info) between the metal and ligands. So how t

Re: [gmx-users] metal_ligand complex

2012-12-03 Thread tarak karmakar
Thanks Justin Yah! We can run steered MD or Umbrella Pulling ( sampling) for this purpose. But one thing I am wondering that how to move the entire complex. In my model there are no covalent bond ( bonding info) between the metal and ligands. So how to select a particular point in the complex to t

Re: [gmx-users] metal_ligand complex

2012-12-03 Thread Justin Lemkul
On 12/3/12 12:09 PM, tarak karmakar wrote: Dear All, In my system, I want to see the binding of a ligand, composed of a divalent metal and 6 ligands, to a protein. I am not sure that movement of this type of complex ( ligand) towards the protein active site cavity can be feasible or not. If