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
Received on Mon Sep 05 2016 - 09:00:03 PDT
