Re: [AMBER] Antechamber on regular nucleotides

From: David A Case <>
Date: Thu, 11 Jun 2015 10:08:42 -0400

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

If you want to see how to run antechamber on polymer fragments, see tutorial

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 GAFF)
are useful in generating an approximate force field if you don't already have
something better; but that is not the case for nucleotides.


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Received on Thu Jun 11 2015 - 07:30:03 PDT
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