[Dock-fans] 5' terminal phosphates

John Irwin jir322 at gmail.com
Wed Dec 31 12:32:18 PST 2014

Hi Amali

I don't have a lot of experience in this area, but I know that
phosphates are challenging for docking because of the high
electrostatic potential and desolvation penalties.  To find the best
protocol, I recommend you approach it as a research question. What do
you know? Does your calculation recapitulate what you already know?
Perform controls to convince yourself that the model is capturing the
most important interactions and contributions.

I don't think there is a cut and dried answer to this question.

Good luck!


On Tue, Dec 30, 2014 at 8:54 PM, Amali Guruge <amaligg2010 at gmail.com> wrote:
> Dear All,
> My enzyme contains DNA molecules. When I prepare the enzyme for docking
> using Chimera "Dock Prep" option, the program gives a message
> "Delete 5' terminal phosphates from nucleic acid chains? The AMBER charge
> set lacks parameters for 5' terminal phosphates, & if retained, atoms in
> such groups will be assigned charges for zero"
> My question is what is the best way to proceed? I mean delete the 5'
> terminal phosphates or assign zero charge for those phosphate terminals?
> I added charges for standard residues using AMBERff12SB and other residues
> using Gasteiger.
> Thank you.
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