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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 05 2016 - 09:30:02 PDT
