AMBER Archive (2009)

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

From: Kristina Furse (Kristina.Furse.1_at_nd.edu)
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 

--
Kristina Furse
Postdoctoral Research Associate
260B Stepan Chemistry Hall
Notre Dame, IN 46556
(574)631-3904
________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of amoreno_at_wesleyan.edu [amoreno_at_wesleyan.edu]
Sent: Thursday, July 23, 2009 10:20 AM
To: AMBER_at_ambermd.org
Subject: [AMBER] Replacing DNA base with analog

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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