Hello,
Thanks for your reply. Conformation dependent partial charges implemented
in openFF have been discussed here
https://chemrxiv.org/engage/chemrxiv/article-details/67579833085116a133e39d86.
I was looking If anything similar was also available for GAFF as well. Also
have a separate question, it is a good idea to use RESP partial
charges calculated from more accurate theory like mp2 instead of HF or
B3LYP along with GAFF bonded parameters.
Best,
Pradip
On Wed, Nov 27, 2024 at 3:46 AM Dr. Anselm Horn via AMBER <amber.ambermd.org>
wrote:
> 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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> >
>
>
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Received on Mon Feb 03 2025 - 11:00:02 PST
