I understand it better now. I'll try again with the suggestions.
Thank You so much for the reply.
Sincerely,
Subhasmita
On Mon, Dec 9, 2024 at 7:36 PM Dr. Anselm Horn via AMBER <amber.ambermd.org>
wrote:
> Subhasmita,
>
> since the procedure described in the tutorial is a complex one, problems
> may arise at every step depending on your input and your system.
> You provided just a large pdb file containing the modified amino acid
> and the main-chain definition file, but no parameter files you created
> and (probably) used.
>
> The error you received is ascribed to a possible faulty connection atom.
> Maybe you want to check these definitions again.
>
> Concerning your question, whether inclusion of a TER card between bonded
> residues was ok:
> leap used the consecutive residues within a chain of an input pdb file
> to construct covalent bonds between the residues; a TER marks an end of
> the peptide chain, resulting in terminating residues at that positions.
> Thus, if you have a PDB file and you insert a TER before and after a
> certain residue, no backbone bond will be created between the then
> isolated amino acid and the then termini of the chain.
>
> Therefore, the inclusion of TER before and after your modified amino
> acid residue will not result in a structure you want: If you visualize
> that structure, you could identify the artificial termini you created:
> residue 45 ends with COO-
> residue 47 starts with +H3N
>
> Maybe it would help you, when you do the single steps of the
> parameterization again and compare the output you obtain with your
> expectations (i.e. sample output from the tutorial).
>
> Maybe that helps.
>
> Good luck,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
>
>
> Am 09.12.2024 um 10:20 schrieb SUBHASMITA MAHAPATRA MAHAPATRA via AMBER:
> > Hi,
> >
> > I am trying to solvate a complex PDB where the 46th SER forms a covalent
> > bond with the ligand. I modified the amino acid to SEJ and following this
> > green fluorescent amber tutorial (
> > https://ambermd.org/tutorials/basic/tutorial5/index.php). I was getting
> > error in the tleap step as follows-
> >
> > teLeap: Error!
> >
> > Comparing atoms
> >
> > .R<CYS 45>.A<C 10>,
> >
> > .R<SEJ 1>.A<H1 2>,
> >
> > .R<SEJ 1>.A<H2 3>, and
> >
> > .R<SEJ 1>.A<H3 4>
> >
> > to atoms
> >
> > .R<SEJ 1>.A<CA 5>,
> >
> > .R<CYS 45>.A<C 10>,
> >
> > .R<SEJ 1>.A<H3 4>, and
> >
> > .R<SEJ 1>.A<H1 2>
> >
> > This error may be due to faulty Connection atoms.
> >
> > !FATAL ERROR----------------------------------------
> >
> > !FATAL: In file [chirality.c], line 140
> >
> > !FATAL: Message: Atom named CA from SEJ did not match !
> >
> > !
> >
> > !ABORTING.
> >
> > However, when I add the TER card between 45th, 46th and 47th residues,
> the
> > error gets resolved. It also generates solvated parameter files. I would
> > like to know if it is okay to add TER between covalent bonded residues.
> >
> > Kindly help me in this regard.
> >
> > Thank you
> >
>
>
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--
*Yours Sincerely*
*Subhasmita Mahapatra*
*Ph.D. Scholar (PMRF)*
*Computational Biophysics Group*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*Madhya Pradesh, India (453552)*
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Received on Mon Dec 09 2024 - 09:00:05 PST
