Dear Adrian and Vinicius,
thank you for the clarification, and also for the suggestion.
I'll forward that to my collegue.
All the best
Anselm
On 03/24/2021 06:22 PM, Adrian Roitberg wrote:
> Hi Anselm.
>
> As Vinicius mentioned, you would need to code inside AMBER to be able to
> do this directly.
>
> If you are interesting mostly on the change in pKa of the compound, you
> can do Free energy calculations for the molecule in solution and in a
> binding pocket for example.
>
> Adrian
>
>
> On 3/24/21 7:58 AM, Dr. Anselm Horn wrote:
>> [External Email]
>>
>> Dear all,
>>
>> a question to the CpHMD experts:
>>
>> Is it possible to apply the constant-pH simulation approach to systems,
>> where the protonated state differs from the deprotonated one in the
>> local structure, i.e. atom types and local parameters in addition to
>> atomic charges?
>>
>> A collegue of mine was interested in investigating such a species, where
>> deprotonation results in a different local structure, going from
>> all-planar to out-of-plane distorsion.
>>
>> As far as I understood the CpHMD approach implemented in Amber, the
>> different protonation states are realized by applying different charge
>> sets and Hydrogen radii to the titratable residue, keeping the
>> perturbation of the system small. And thus, no further change besides
>> atomic charges and the presence or absence of H atoms could be taken
>> into account.
>>
>> Is this correct? Or are there some advanced options, e.g. to switch
>> between complete topology files?
>>
>> Best regards
>>
>> Anselm
>>
>>
>>
>>
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Received on Thu Mar 25 2021 - 01:30:02 PDT
