[AMBER] Unnatural nucleic acid in DNA chain

From: Anthony Bogetti <anthony.bogetti.gmail.com>
Date: Thu, 24 Jan 2019 15:52:19 -0500


I'm trying to run a MD simulation with a small DNA molecule that contains
an edited nucleotide (it's basically an Adenine without the base). For
instance, my molecule is AXA where X is just the deoxyribose sugar. How
would you suggest going about generating force field parameters for X? I
tried following the tutorial here (
http://ambermd.org/tutorials/basic/tutorial4b/index.html) for using
Antechamber for this, but I'm getting errors saying I have a one-sided
connection and related errors to this about leap not being able to find
bond parameters for the bond between the two nucleotides. Even when I
manually add these connections into the lib file, I still get some boned
and angle errors relating to the atom types between my two nucleotides A
and X. Do you have any suggestions?

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Received on Thu Jan 24 2019 - 13:00:01 PST
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