Thanks, Carlos!
So, that is already the second opinion favouring macromolecular AMBER terms for the nucleotide part. It sounds like using GAFF for the whole residue is not a good idea...
Krisztina
--- On Thu, 9/20/12, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] modified nucleotide
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Thursday, September 20, 2012, 5:59 PM
I can't give specific help, but would just add to this some further
clarification- it is probably very important to keep the existing Amber
terms for things such as the DNA backbone. You need to make sure to keep
the same atoms types in your new fragment so that the old dihedral terms
get applied. You probably should restrict changes in the partial charges to
the area where you attach the amino acid (keep the backbone and glycosidic
angle area the same charges, or else the old dihedral terms aren't
appropriate any more). .
On Thu, Sep 20, 2012 at 11:53 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Krisztina,
>
> > I would like to run MD on a DNA 14mer containing a modification on a
> > base: a covalently attached amino acid. My question is: can I use
> > GAFF atom types and parameters derived with antechamber and add to
> > the AMBER ff? The critical part is probably the linker connecting
> > the nucleotide to the amino acid. Can the AMBER ff and small organic
> > GAFF types be used together or I need parameter optimisation?
>
> You will have to generate a molecular fragment starting from a whole
> molecule.
> Thus, you might be interested in using R.E.D. at q4md-forcefieldtools.org.
> You will find tutorials there as well.
>
> As you will use the last version of the Amber FF for nucleic
> acids/proteins my feeling is that you should keep using this FF for
> your modified nucleoside/tide as well; i.e. I would not use GAFF.
>
> regards, Francois
>
>
>
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Received on Thu Sep 20 2012 - 13:00:02 PDT
