On Thu, Apr 12, 2018, Edjan Silva wrote:
> I would like to perform a moleuclar dynamic simulation between a DNA
> fragment and a small molecule. Just to analyze the conformational
> variation of the molecule, before the DNA.
>
> Which parameters should I use?
> For example:
> leaprc.DNA.bsc1 ??
> leaprc.water.tip3p ?? ...
Above look like reasonable parameters for water and DNA. You will need
also to get parameters for your small molecule: See the antechamber
section of the manual, or the following tutorial for help:
http://ambermd.org/tutorials/basic/tutorial4b/index.html
...good luck....dac
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Received on Thu Apr 12 2018 - 10:00:03 PDT
