Pradip,
gaff parameters do not depend on the actual molecular conformation, they
are general.
However, atomic charges do not belong to the gaff parameter set, and
depending on the charge scheme used, the conformation will have an
influence on their value.
Note, that you could in principle create different residues for the same
molecular entity in different conformations with the same gaff
parameters (i.e. atom types) but with different atomic charges.
This was a decision between a general or special parameter set. The
latter might be argued for, if the conformations (and thus the charges)
differ to a large extend and do not convert into each other, i.e. exist
as separate species during the simulations.
But I am not aware of such an approach.
Traditionally it is one entity, one parameter set.
Thus, you could use more than a single conformation for charge
generation (cf the RESP charges for amino acids, where alpha-helical and
beta-sheet conformation were used), but create a single set of atomic
charges.
Maybe that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 26.11.2024 um 18:34 schrieb Pradip Si via AMBER:
> Hello,
> I have a general question regarding gaff parameterization. I want to run MD
> with GAFF for a conformational polymorphic crystal with many conformations.
> Should I parametrize for one conformation and use the same for other
> conformations or Is there any correct way to parameterize GAFF in case of
> multiple conformations?
>
> Best Regards,
> Pradip Si
> PhD Student
> UNT, Texas
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Received on Wed Nov 27 2024 - 02:00:02 PST
