On Tue, Oct 04, 2022, Miroslav Suruzhon via AMBER wrote:
>
>
> I have been trying to use AMBER to perform a residue perturbation using
> the TI code. As far as I understand, if one is working with e.g. a
> tripeptide such as (using one-letter amino acid codes) PTG and wants to
> perturb it to PYG, the correct way to do it in AMBER is to generate a
> composite residue (which we will call MUT), which results in P-MUT-G,
> where MUT contains atoms from both T and Y. Then one sets the TI masks to
> be all the corresponding atoms from the MUT residue, and the SC masks
> define the dummy atoms as usual.
It's unclear how you created the MUT residue: can you outline the process
you used?
The "usual" method is to use the timerge action in ParmEd. See section 15.2
of the Reference Manual.
...thanks....dac
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Received on Wed Oct 05 2022 - 07:00:02 PDT
