sorry it took so long to reply to this, I was traveling for a while.
Dave is right about this, and after doing some checking I see that the
actual FF files contain CT not 2C as is stated in the paper's SI. I believe
that they were made 2C originally to differentiate dihedral fitting, but it
turned out that this wasn't needed for the aromatics since they already had
unique sets of 4 atom types for these dihedrals without needing to change
atom type.
carlos
On Tue, Jul 9, 2019 at 10:54 AM David Cerutti <dscerutti.gmail.com> wrote:
> It's not clear from your mail where you find the atom listed as "CT" and
> what you are comparing. The atom type of the beta carbon is indeed CT for
> those two amino acids in the amino12.lib file, but if there is an error
> it's almost certainly in the manual, not the force field itself. The force
> field atom typing got branched as a matter of necessity when researchers
> found that differentiation of the various amino acids was necessary to
> reproduce Chi1 and Chi2 angle profiles.
>
> I don't know what level of automation and integration among the various
> amino acids (i.e. fitting all parameters for all amino acids
> simultaneously) Simmerling group had when they made their side chain
> parameters back in 2011-2012. Today, have the means to completely
> integrate the parameter development, branch atom types, and monitor which
> parameters apply to which amino acids in the mdgx package, but it does not
> write manuals for us.
>
> DSC
>
>
> Dave
>
>
> On Tue, Jul 9, 2019 at 10:42 AM Dylan Tasse <catrixs01.hotmail.com> wrote:
>
> > Hi,
> >
> > I'm writting to you today because I need some precision about the
> > parameters in Amber ff14SB.
> >
> > I gave you on this email a screenshot of page 8 and 9 in the supporting
> > information of amberff14SB which discribe the parameters of ff14SB.
> >
> > On page 8 and page 9, you can see the amino acid PHE and TYR. They say
> > that the bêta carbon "CB" is a atom type of 2C as you can see (I
> > highlighted in red for more clarity).
> >
> > But in fact, on amberff14sb, it is still an atom type of CT when I
> > compare...
> >
> > So my question is: Why did they not change the atom type? Is that an
> error
> > ?
> >
> > Thank you some much for your time and have a great day
> >
> > Dylan
> >
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> >
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Received on Tue Jul 09 2019 - 08:30:03 PDT
