AMBER Archive (2009)

Subject: RE: [AMBER] Replacing DNA base with analog

From: Kristina Furse (
Date: Thu Jul 23 2009 - 09:36:26 CDT

Maybe check your prep file for the base analog and make sure it has connect0/connect1 information? I forget exactly how it works, but you can find info on it in the leap section of the manual. If I remember correctly, these things tell leap how to connect the backbone between residues.

Good luck!

Kristina Furse
Postdoctoral Research Associate
260B Stepan Chemistry Hall
Notre Dame, IN 46556
From: [] On Behalf Of []
Sent: Thursday, July 23, 2009 10:20 AM
Subject: [AMBER] Replacing DNA base with analog


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


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