Krisztina,
> keeping the macromolecular parameters for the standard amino acid
> and nucleotide part sounds sensible to me, but the linker is a
> problem: for charges you suggest RED (thanks for the link!), but
> where do I get the rest of the parameters?
R.E.D. will do the job i.e. derive the charge values for the fragment
and generate the force field (FF) library.
Then, you will have to add the FF atom types; and define the connecting atoms.
> The alternative is, that Antechamber could make an internally
> consistent new residue in GAFF, which is then used together with
> macromolecular AMBER ff residues....
I think you need a fragment in agreement with force field types as
defined in parm99.dat and not as in GAFF; i.e. using capital letters.
regards, Francois
> --- On Thu, 9/20/12, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] modified nucleotide
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Thursday, September 20, 2012, 5:53 PM
>
> 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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>
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Thu Sep 20 2012 - 13:30:02 PDT
