[AMBER] teLeap: Error! Atom named CA from SEJ did not match !

From: SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <amber.ambermd.org>
Date: Sat, 7 Dec 2024 16:16:53 +0530

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. I am following this
green fluorescent amber tutorial (
https://ambermd.org/tutorials/basic/tutorial5/index.php). However, I am
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.

The main chain file (sej.mc) was generated from the attached pdb file.

Kindly anyone help with this error.

Thank you 

-- 
*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 Sat Dec 07 2024 - 03:00:02 PST
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