[AMBER] Cyana3.97 to Amber15 pdb conversion

From: Erik Davis <erikd.g.clemson.edu>
Date: Wed, 3 Aug 2016 11:09:35 -0400

Dear all:

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,
http://ambermd.org/tutorials/basic/tutorial1/, 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

Any help on this cyana to amber pdb conversion problem is greatly


Erik V. Davis
Clemson University
Pāndēng shānmài
"Only one who attempts the absurd can achieve the impossible"
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Received on Wed Aug 03 2016 - 08:30:02 PDT
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