you might try reaching out to Yong Duan directly, I don't know how active
he is own the Amber list.
On Mon, Sep 5, 2016 at 12:05 PM, Mark Abraham <mark.j.abraham.gmail.com>
wrote:
> Hi,
>
> Thanks for the response. It seems that amber03 had LYN charge parameters
> that changed at some point in the AMBER program prep files, perhaps as a
> fix. But it is hard for me to find the reason for the change, to know
> whether e.g. the GROMACS implementation is wrong because we copied the old
> version and haven't known to stay in sync. This apparently does affect LYN
> in amber03, but maybe other things got fixed in AMBER alongside that fix,
> and this would also need attention in GROMACS. If there was a publicly
> readable source code repository then I could search it, but I don't think
> that exists.
>
> Mark
>
> On Mon, Sep 5, 2016 at 5:57 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > It's not clear what you're asking when you say AMBER's definition. The
> > partial charges are different between ff03, ff99SB/ff14SB and ff14ipq,
> > among others. Are you asking what the charges should be for each model?
> > Each ff implementation in gromacs should match that models, but each ff
> > does not match the other. Also many ff do not really have parameters for
> > alternate protonation states or otherwise modified amino acids. In that
> > case people may use something, but it may not have been defined in the
> > papers meaning parameters were never optimized. What you get may depend
> on
> > what other force field listing a user had in their input.
> >
> > On Sep 5, 2016 11:41 AM, "Mark Abraham" <mark.j.abraham.gmail.com>
> wrote:
> >
> > Hi,
> >
> > Historically, amber99sb and amber03 had the same charges for LYN (e.g.
> > http://dev-archive.ambermd.org/200406/0002.html), but in AMBER 14 and 16
> > they differ (see report by a GROMACS user at
> > https://redmine.gromacs.org/issues/2046). The amber03 paper
> unfortunately
> > doesn't give any parameters for LYN (
> > http://ffamber.cnsm.csulb.edu/ffamber/pdfs/duan_AMBER03_2003jcc.pdf). Is
> > there another / canonical source for the LYN parameters? Can anyone
> confirm
> > that there was a change in AMBER's definition at some point? Were there
> any
> > other changes alongside those for LYN?
> >
> > I'd like to keep the AMBER and GROMACS implementations of AMBER force
> > fields in step with such fixes - is there any easy way to find what
> changes
> > have taken place in AMBER over the years?
> >
> > Thanks!
> >
> > Mark
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Received on Mon Sep 05 2016 - 10:00:02 PDT
