Re: [AMBER] Force field interfaces

From: Piia Bartos via AMBER <amber.ambermd.org>
Date: Fri, 17 Jun 2022 12:26:24 +0000

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 Barto¹, 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>
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<mailto: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 Barto¹, 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><mailto:piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>>
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Received on Thu Aug 04 2022 - 13:32:00 PDT
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