Hi Baifan,
we will send you the ff99 + bsc0 + ε/ζOL1+ χOL4 leaprc file for Amber 14 to
your e-mail.
Alternatively, you could find the ε/ζOL1 parameters in supporting
information of Zgarbova et al., JCTC 2013, 9, p2339 and χOL4 parameters in
Krepl, Zgarbova et al., JCTC 2012, 8, p2506. SI files contain all that is
necessary to make the ff99 + bsc0 + ε/ζOL1+ χOL4 combination, however, it
takes some time to make your own leaprc file.
Best regards
Petr
On Mon, Nov 24, 2014 at 3:55 PM, Baifan Wang <ferlich.comput.gmail.com>
wrote:
> Dear Amber Users,
>
>
>
> I currently start to simulate the DNA G-quadruplex. The manual of Amber14
> recommends that the combination of ff99 + bsc0 + ε/ζOL1+ χOL4 forcefields
> would have better performance.The manual indicated that, “The appropriate
> leaprc file will be made available soon as an update to AmberTools.”. My
> AmberTools has been updated to the nearest version, it seems that the
> leaprc file is still unavailable. So how can I employ these force field to
> my simulation?
>
>
>
> With kind regards,
>
>
>
> Baifan Wang
>
>
>
> Kemijski inštitut
> Ljubljana
> Slovenija
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Received on Tue Nov 25 2014 - 02:00:02 PST
