Re: [AMBER] unexpected missing parameters for protein atoms?

From: Vaibhav Dixit <>
Date: Fri, 30 Jul 2021 19:25:26 +0530

Dear David and Amberites,
I think Chimera added a TER line between the protein chain and the next
modified residue CM1.
After removing the TER line it worked as expected.
I'm planning to automate a workflow for selected mutant complexes, thus
didn't pay much attention to the PDB file.
But I guess one can't ignore it totally. Just wondering why
pdb4amber didn't/couldn't fix it?

Can you please suggest which tools can be used to create selected mutants
automatically (via command-line) which can then be used in tleap to
generate files for MD and subsequently analysis?
thanks for the insightful comments and quick response.


Dr. Vaibhav A. Dixit,

Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,


NCBI bibliography:

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On Fri, Jul 30, 2021 at 6:34 PM David A Case <>

> On Fri, Jul 30, 2021, Vaibhav Dixit wrote:
> >I'm getting the following errors after mutating a Phe393 to Ala and there
> >is no other change in the structure.
> >
> >/usr/local/amber18/bin/teLeap: Warning!
> > Converting N-terminal residue name to PDB format: NLEU -> LEU
> >
> >/usr/local/amber18/bin/teLeap: Warning!
> > Converting N-terminal residue name to PDB format: NILE -> ILE
> >
> >/usr/local/amber18/bin/teLeap: Warning!
> > Converting C-terminal residue name to PDB format: CLEU -> LEU
> Check the above: it looks like you may have an unwanted break in the
> polypeptide chain, leading to an unwanted N-terminal residue. (A guess:
> is phe383 followed by in ILE residue?)
> >/usr/local/amber18/bin/teLeap: Error!
> >Could not find bond parameter for: C - N3
> This (and the other errors) suggest that you are somehow trying to connect
> a
> residue to its neighbor, but you have an N-terminal residue (with N3 as its
> nitrogen) rather than a regular one.
> Hope this helps to locate the problem. If you hand-edited your PDB file,
> double check that everything is OK: in particular that chainID's and
> residue
> numbers are all completely consistent. You may need to try a mutation on a
> short peptide to see if you can get a similar problem, since it will be
> easier to debug there.
> ....dac
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Received on Fri Jul 30 2021 - 07:00:01 PDT
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