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 - 15:00:02 PDT
