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

From: David A Case <>
Date: Wed, 3 Aug 2016 17:41:13 -0600

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.


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Received on Wed Aug 03 2016 - 17:00:04 PDT
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