Okay. Tutorial gives an example using protein with ff99SB force field. I
want to make molecular dynamics using DNA, so use parm99 force field?
2018-04-12 13:58 GMT-03:00 David A Case <david.case.rutgers.edu>:
> 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 Mon Apr 16 2018 - 06:00:05 PDT
