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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Received on Mon Dec 09 2024 - 06:30:03 PST
