RE: [AMBER] Replacing DNA base with analog

From: Kristina Furse <Kristina.Furse.1.nd.edu>
Date: Thu, 23 Jul 2009 15:36:26 +0100

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.ambermd.org [amber-bounces.ambermd.org] On Behalf Of amoreno.wesleyan.edu [amoreno.wesleyan.edu]
Sent: Thursday, July 23, 2009 10:20 AM
To: AMBER.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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jul 23 2009 - 10:09:44 PDT