Thanks Lin.
I tried it
but then I have problem with characterization of the rest of molecule in
the bold part:
H
|
*H2N-C *-C- R2
|| |
O NH-CO-R
Petro
On Sat, Mar 14, 2020 at 10:33 PM Song, Lin <songlin3.chemistry.msu.edu>
wrote:
> Hi,
>
> Maybe when you generate the mol2 and frcmod file for the modified aa, you
> can use AMBER atom type.
>
> Best,
> Lin
>
> > On Mar 14, 2020, at 5:21 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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