Re: [AMBER] Cyana3.97 to Amber15 pdb conversion

From: Erik Davis <>
Date: Fri, 5 Aug 2016 14:01:46 -0400

Thank you for your responses. We are presently making some progress.
Hopefully, a solution has presented itself. If not, or as needed, I will
definitely provide more information.

Thank you!

On Wed, Aug 3, 2016 at 7:41 PM, David A Case <> wrote:

> On Wed, Aug 03, 2016, Erik Davis wrote:
> >
> > We are attempting to refine NMR-derived structures of 9-bp DNA sequences.
> > NMR ensembles employing NOE and torsion restraints were calculated using
> > CYANA 3.97 energy minimization software. The DNA tutorial,
> >, was used for as the basis
> > for our refinement protocol using Amber15 and Ambertools software.
> However,
> > we have encountered issues when converting a CYANA pdb to an AMBER pdb.
> >
> >
> > The problem essentially hinges on the ability to produce usable prmtop
> and
> > inpcrd files for minimization. While we have successfully converted a
> cyana
> > pdb to an amber compatible pdb from which the prmtop and inpcrd files
> were
> > successfully generated without errors, the resulting refined pdb produces
> > many bonding errors in the phosphate backbone as well as in between
> > adjacent intra-strand bases and in some cases truncates the minimization
> > entirely.
> Just to add some notes to what Dan already said:
> 1. Note that the cyanapdb_to_amberpdb script (not clear if this is what you
> are using or not....) is a scaffold: you have to edit certain lines to
> match your particular problem. See the comments in the script itself.
> 2. If you get prmtop and inpcrd files from tleap that seem to be OK (no
> errors), do a minimization without any NMR restraints. See what happens.
> This will help determine whether the problems you are seeing are related to
> the NMR restraints or not.
> But I second Dan's suggestion: we need more details about what you did.
> ....dac
> _______________________________________________
> AMBER mailing list

Erik V. Davis
Clemson University
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"Only one who attempts the absurd can achieve the impossible"
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Received on Fri Aug 05 2016 - 11:30:02 PDT
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