Dear Abhishek,
I think it is the problem of your visualization software. You just load
your topology and co-ordinate file in the visualization software and then
check is there any separation or not. I think you are using chimera. If
your co-ordinate files are also showing gap then you have some problem in
your input files.
On Tue, Apr 10, 2018 at 3:24 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi everyone,
>
>
> I am making oxidized and reduced form of amino acids by making them
> heteroatom. But after making a parameter file when I am visualizing the
> structure it looks like oxidized/reduced amino acid is not a part of
> protein. It is a separate ligand (attached image before.png and after.png)
>
>
> If I remove the TER before heteroatom it is not giving any problem. But
> amber automatically add ter after heteroatom.
>
>
> Please suggest me what should I do.
>
>
>
> Thanking you,
>
> -Abhishek
>
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>
--
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Mon Apr 09 2018 - 20:30:01 PDT
