Hi Lin.
Sorry i did not realize that list uses simple txt and tried to highlight
it by making bold font.
That is H2N-C part and its connections.
H
|
H2N-C-C- R2
|| |
O NH-CO-R
Petro.
On Sat, Mar 14, 2020 at 10:56 PM Song, Lin <songlin3.chemistry.msu.edu>
wrote:
> Hi,
>
> What is the bold part? The picture you attach is not clear to me.
>
> Best,
> Lin
> On Mar 14, 2020, at 5:43 PM, Petro <subscribe.khoroshyy.net<mailto:
> subscribe.khoroshyy.net>> wrote:
>
> 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
> <mailto: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<mailto:
> 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
