[gmx-users] terminal phosphate residue for dna simulations

Vedat Durmaz durmaz at zib.de
Tue Feb 19 14:35:30 CET 2013

hi guys,

does anyone know about a way to simulate mono- or polynucleotides along 
with a 3' or 5' bound monophosphate using an amber force field like 

i couldn't find any residue definition for a terminal phosphate group 
such as " P3' " or " P5' " (exemplarily). do they indeed not exist or am 
i just not able to search them?

thanks in advance & take care

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