Perfect, thank you so much, I think it is an error in the manual too.
Thank you again it helped me
Dylan
________________________________
De : David Cerutti <dscerutti.gmail.com>
Envoyé : 9 juillet 2019 10:53
À : AMBER Mailing List
Objet : Re: [AMBER] amber14sb.ff
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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 09 2019 - 08:30:02 PDT
