Hello,
I'm looking to simulate a small DNA double helix with one of the base pairs
replaced with a certain small molecule. I have already parameterized the
"unnatural" base following the amber tutorials.
However, I am having trouble generating a full structure of my DNA double
helix with the small molecule attached. I've tried creating the DNA
molecule in Avogadro and then manually editing the relevant base pair, but
I get atomtype issues when trying to generate the topology files in leap.
What would be the best way to generate my DNA model with the "unnatural"
base pair? How can I do so in a way that preserved amber atomtypes (for
any forcefield; that doesn't matter at this point).
Thanks,
AB
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 18 2018 - 09:00:04 PST
