They are mixed. You do need to be careful about combining for fields, but
most of the ones included in Amber are designed to be mixed like this.
There is a good description at
http://ambermd.org/AmberModels.php
On Fri, Jun 17, 2022, 8:26 AM Piia Bartos <piia.bartos.uef.fi> wrote:
> Yes, I am thinking about these kind of interactions:
>
>
>
> Lets assume there is an O atom in DNA and in a protein. When counting the
> non-bonded interaction between these atoms, the partial charges and LJ
> radius are needed. Are these parameters taken from the DNA force field or
> from the protein force field? Or are the parameters mixed so that each atom
> takes them from their own force field?
>
>
>
> Cheers,
>
> Piia
>
>
>
> --
>
> Piia Bartoš, Ph.D. (Pharmacy)
>
> Project Researcher
>
>
>
> University of Eastern Finland | UEF | School of Pharmacy
>
> Kuopio Campus | Canthia
>
> Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
>
> +358 50 548 8376 | piia.bartos.uef.fi
>
>
>
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* perjantai 17. kesäkuuta 2022 14.40
> *To:* Piia Bartos <piia.bartos.uef.fi>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] Force field interfaces
>
>
>
> Can you be more specific about what you are looking for?
>
>
>
> On Fri, Jun 17, 2022, 6:46 AM Piia Bartos via AMBER <amber.ambermd.org>
> wrote:
>
> Hi,
>
> Amber deals with different molecules (protein, RNA, DNA, small
> molecules..) in different force fields. How are the interfaces between
> different force fields dealt with? Could you point me to some literature
> about this?
>
> Cheers,
> Piia Bartos
>
>
> --
> Piia Bartoš, Ph.D. (Pharmacy)
> Project Researcher
>
> University of Eastern Finland | UEF | School of Pharmacy
> Kuopio Campus | Canthia
> Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
> +358 50 548 8376 | piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>
>
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Received on Thu Aug 04 2022 - 13:32:06 PDT
