Re: [AMBER] Antechamber on regular nucleotides

From: <>
Date: Fri, 12 Jun 2015 06:38:48 +0000

In this case you would go with a fragment/residue based approach. You keep the parameters for those parts you already have and find parameters only for those bits you don't have yet. Have you looked into tutorial B5 already?

From: Mrinda Jones []
Sent: 12 June 2015 06:58
To: AMBER Mailing List
Subject: Re: [AMBER] Antechamber on regular nucleotides

Hi David,

To pacify your wondering hunger :-), I would like to mention I am doing
this to create modified nucleotide libraries. Every sugar ring of each
nucleotide of DNA which I am dealing with is modified. So, I was thinking
that calculating the partial charges of each nucleotide and then joining
them (using set head/ tail) to form a double helix will solve the problem.
Is this approach right? If yes, then Is it fine to calculate partial charge
of fragments i.e. DA DT DC DG as per amber library or I have to calculate
partial charges after making them complete molecule rather than taking them
as a fragment?


On Thu, Jun 11, 2015 at 7:38 PM, David A Case <>

> On Thu, Jun 11, 2015, Mrinda Jones wrote:
> > I am trying to prepare prepin files for regular nucleotides (i.e. DA DT
> DG
> > DC) with the use of command:
> > antechamber -i DX.pdb -fi pdb -o DX.prepin -fo prepi -c bcc -j 4 -at
> amber
> > -nc -1
> >
> >
> > I got required pdb files from tleap as :
> > >savepdb DA DA.pdb
> This won't work: the "DA" unit is not a complete molecule (rather, it is
> a fragment that is intended to be included in a oligonucleotide.) But
> antechamber wants its input PDB file to represent a complete, separate
> molecule.
> If you want to see how to run antechamber on polymer fragments, see
> tutorial
> B5.
> I can't end without wondering why you want to do this in the first place.
> The
> standard Amber libraries for nucleotides have been highly tweaked and
> extensively tested, and will be much better than the default force field
> that
> antechamber would be able to generate. Remember that antechamber (and
> are useful in generating an approximate force field if you don't already
> have
> something better; but that is not the case for nucleotides.
> ....dac
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