Dear Nihal,
have you received the parameters all right now?
Regards
Petr
On Sun, Feb 1, 2015 at 8:25 PM, Nihal Korkmaz <enihalkorkmaz.gmail.com>
wrote:
> Dear Baifan,
>
> I saw on amber forum that they sent you the leaprc file, I emailed the
> group but no one responded so far. I would highly appreciate if you
> would please send that leaprc file to me?
>
> Thank you,
> Nihal Korkmaz
>
> On 11/25/14 6:29 AM, Baifan Wang wrote:
> > Dear Petr,
> >
> > Thank you very much for your kind help.
> >
> > With kind regards,
> >
> > Baifan
> >
> > 2014-11-25 10:52 GMT+01:00 Petr Jurecka <jureckap.gmail.com>:
> >
> >> 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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> >>>
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> >>
> >
> >
>
>
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Received on Wed Feb 04 2015 - 07:00:02 PST
