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

From: David A Case <>
Date: Fri, 30 Jul 2021 09:03:47 -0400

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.


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Received on Fri Jul 30 2021 - 06:30:02 PDT
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