Hi,
We need some more information before we can help. Can you list the
exact steps you tried (i.e. commands, flags, input) and any relevant
output messages (warnings, errors, etc). Thanks,
-Dan
On Wed, Aug 3, 2016 at 9:09 AM, Erik Davis <erikd.g.clemson.edu> wrote:
> 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
> entirely.
>
>
> Any help on this cyana to amber pdb conversion problem is greatly
> appreciated.
>
>
> Respectfully,
> ------------------------------
>
>
> --
> Erik V. Davis
> Clemson University
>
> 攀登山脉
> Pāndēng shānmài
>
> "Only one who attempts the absurd can achieve the impossible"
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Aug 03 2016 - 12:30:03 PDT
