I have checked it with VMD and still same problem.
I have a modified amino acid, which I have named as CY2. Then I have optimized and generated frcmod and lib files for it. Then while making a solvated complex I want this CY2 N terminal to be bonded to ser C terminal and C terminal of CY2 with N terminal of Ile. As without giving bond command I am not having issue but CY2 looks like a separate ligand, not a part of a protein (attached pic in previous email). But when I am giving a bond command it is asking for
Could not find bond parameter for: C - n1
Could not find bond parameter for: c2 - N
Building angle parameters.
Could not find angle parameter: O - C - n1
Could not find angle parameter: C - n1 - c2
Could not find angle parameter: CX - C - n1
Could not find angle parameter: n1 - c2 - N
Could not find angle parameter: o - c2 - N
Could not find angle parameter: c2 - N - H
Could not find angle parameter: c2 - N - CX
Could not find angle parameter: c2 - c2 - N
Building proper torsion parameters.
** No torsion terms for O-C-n1-c2
** No torsion terms for CX-C-n1-c2
** No torsion terms for n1-c2-N-H
** No torsion terms for n1-c2-N-CX
** No torsion terms for o-c2-N-H
** No torsion terms for o-c2-N-CX
** No torsion terms for c2-c2-N-H
** No torsion terms for c2-c2-N-CX
So the I have made CY2 structure with N and C terminal bonded to Ser and Ile C and N terminal. Then I have generated lib and frcmod file, still I am getting same error.
please suggest me how to solve this issue.
Thanking you,
-Abhishek
________________________________
From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Sent: Monday, April 9, 2018 4:21:11 PM
To: AMBER Mailing List
Subject: Re: [AMBER] residue looks like it is not a part of protein
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 Thu Apr 12 2018 - 09:00:02 PDT
