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
--
*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 - 01:30:04 PST
