Hi David,
I wasn’t aware of this function - I tried it now and it seems to work. Many thanks!
Kind regards,
Miro
Miroslav Suruzhon MSc PhD
Molecular Dynamics Research Scientist
+44 (0) 7719 025700
Exscientia
The Schrödinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE
> On 5 Oct 2022, at 14:39, David A Case <david.case.rutgers.edu> wrote:
>
> 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 Mon Oct 10 2022 - 03:30:02 PDT
