this looks to me like a mismatch in the atom info on your input pdb and the
lib file.
- check to see if the pdb contains coordinates for all of the atom in your
modified amino acid
- make sure the lib file atom names match up with the pdb file
- check the leap log file carefully for any warnings
- unrelated to the structure problem, but important anyway: make sure your
lib file is consistent with the force field you are using for the modified
amino acid. often people find a library file and use it with a protein
force field, but they may not have consistent parameter
development (perhaps different charge models and so on).
On Mon, Jul 3, 2023 at 1:21 PM Singh, Swapnil via AMBER <amber.ambermd.org>
wrote:
> Hi,
> I am currently performing a site-specific mutation on a protein's helix
> using an unnatural amino acid. During the process of adding ions and water
> molecules to the system utilizing the tleap program, I observed that the
> mutated probe is not maintaining its helical structure and is experiencing
> a disruption or unwinding in the middle. It is important to note that there
> are no apparent errors in the tleap file. I also have a lib file for
> unnatural amino acid. I am seeking assistance to understand the underlying
> cause of this issue and to explore potential solutions to rectify it. Any
> guidance or insights would be greatly appreciated.
>
> [cid:b873814a-8f95-4b91-8b37-02028cc9bd7b]
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>
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Received on Mon Jul 03 2023 - 10:30:02 PDT
