Hello,
I recently started to work with amber force fields and, first of all, I
would like to say that section 14.1 of the Amber 2020 manual that
explains the parameter files is really helpful. But we had quite some
confusion with section 14.1.7. about the non-bonded terms. After
Eq.(14.8) it says "Rmin is the sum of the van der Waals radii, Ri+Rj..."
which is fine, but then in the caption of Fig. 14.2 it says that Rmin =
1.908 Ang for the c3 atom. I believe this should be Ri and, in this
case, Rmin = 2*Ri.
Then, in Eq.(14.13), there is Rmin,i,j = 0.5(Rmin,i+Rmin,j), so then, in
this case, it should be Rmin = 2*Rmin,i,j = Rmin,i+Rmin,j = Ri+Rj.
Furthermore, in the text following Eq.(14.14), it says that in the
parameter file [Rmin,\epsilon] are given, but again, I believe, this
should be Ri.
Also, after Eq.(14.12) it say: "Van der Waals data in Amber force fields
are given for each atom as a single data pair, a radius Rmin (’van der
Waals’ radius in Ang) and an energy \epsilon (kcal/mol) representing the
depth of the potential well." So, when we were using Eq.(14.12) to
compute A from \epsilon and Rmin, we first used the 'Rmin' given in the
parameter file, instead of 2*Rmin.
Unless we have some other confusion in this, it would be great if you
could adjust the manual and maybe use, for example, Rvdw or something
else as a variable for the van der Waals radii that are given in the
parameter file and then Rmin only for the parameter entering Eq.(14.8).
Thanks,
Jutta
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Received on Mon Apr 19 2021 - 09:00:02 PDT
