when you generated the frcmod and lib file, it assumed that it was a
separate molecule. the error messages you are getting indicate that it does
not have parameters for the cross terms at the connection between your
molecule and the standard protein amino acids. that is because you did not
generate these when you fit parameters for the isolated CY2. Without these
parameters you cannot proceed with simulations.
you might want to look at this tutorial if you have not done so already:
http://ambermd.org/tutorials/basic/tutorial5/index.htm
On Thu, Apr 12, 2018 at 11:41 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> 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
