[Dock-fans] 5' terminal phosphates

Amali Guruge amaligg2010 at gmail.com
Tue Dec 30 20:54:29 PST 2014

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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