Keep in mind that you need AmberTools 1.5 in order to access ff10 (but it's
recommended that you upgrade, anyway). You can install AmberTools 1.5
alongside Amber10 (and indeed, as force fields and PDB standards change,
it's good to stay current with AmberTools).
All the best,
Jason
On Fri, Aug 12, 2011 at 9:41 AM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Aug 08, 2011, manikanthan bhavaraju wrote:
>
> > I am trying to prepare prmtop and inpcrd files for uncomplex DNA-22mer
> using
> > xleap of amber10. I have downloaded the pdb file from the protein data
> bank
> > and made required modification. Still xleap is unable to save the files,
> as
> > it is complaining about the atom type. Attached is the modified pdb
> > file. I never handled DNA stuff with amber any suggestions.
>
> You file works fine for me. Did you use leaprc.ff10? Here were my
> commands:
>
> tleap -f leaprc.ff10
> x = loadpdb DNA_aptamer.pdb
> saveAmberParm x prmtop inpcrd
>
> ....dac
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 12 2011 - 08:00:02 PDT
