it helps if you focus on just the atom types across the bond, not extra
ones as in your example.
once you make a list of atoms that saw the gaff atom type and non-GAFF
(this depends on which force field, you don't say)
you just find the one that has the normal force field atom types that match
your atoms.
in your case n maps to N, c3 to CX, and c to C. so C -n -c3-c should be the
same as C-N-CX-X
On Sat, Mar 14, 2020 at 5:22 PM Petro <subscribe.khoroshyy.net> wrote:
> Hi.
> I made an modified amino acid in GAFF.
> Now I am trying to connect it to an a AMBER peptide.
>
> AMBER peptide bond atom types looks like
> |
> C - CX - N - C -CX
> || | | ||
> O H H O
>
> in modified case it will look like:
> c3
> |
> c- c3 - n - C -CX
> || | | ||
> o h1 hn O
>
> leap requesting to provide these
> C -n -c3-c
> C -n -c3-c3
> C -n -c3-h1
> torsions.
> But I somehow
> I was searching by analogy for
> C-N-CX-(H,CX,C)
> in par10.dat
> But I cannot see anything suitable.
> Any suggestions?
> Does it make sense, at all what I do?
> Thanks.
> Petro.
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Received on Sat Mar 14 2020 - 15:30:02 PDT
