AMBER Archive (2009)

Subject: [AMBER] Replacing DNA base with analog

From: amoreno_at_wesleyan.edu
Date: Thu Jul 23 2009 - 09:20:08 CDT

Hello,

I am trying to preform a 10ns molecular dynamics simulation on duplex DNA
containing a base analog. I have the frcmod for the base analog
nucleotide and the prep file. I have tried deleting all atoms for the
base I want to replace and changing the backbone atoms name to that of the
analog. I then ran this through tLEAP. The result was tleap generating a
file with the base not bonded to the backbone. Does anyone have any
suggestions? or a better way to insert a base analog into the DNA

thanks

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